The Educational Implications of Regionalisation.

ERIC Educational Resources Information Center

Macdonald, R.

As of May 1975 the structure of Scottish local government will experience a change that will affect rural education, as districts will be reorganized for purposes of encouraging local control. In reference to this new structuring, the following questions must be considered: (1) Since it has been claimed that existing small school authorities lack…

Mapping the Small Molecule Interactome by Mass Spectrometry.

PubMed

Flaxman, Hope A; Woo, Christina M

2018-01-16

Mapping small molecule interactions throughout the proteome provides the critical structural basis for functional analysis of their impact on biochemistry. However, translation of mass spectrometry-based proteomics methods to directly profile the interaction between a small molecule and the whole proteome is challenging because of the substoichiometric nature of many interactions, the diversity of covalent and noncovalent interactions involved, and the subsequent computational complexity associated with their spectral assignment. Recent advances in chemical proteomics have begun fill this gap to provide a structural basis for the breadth of small molecule-protein interactions in the whole proteome. Innovations enabling direct characterization of the small molecule interactome include faster, more sensitive instrumentation coupled to chemical conjugation, enrichment, and labeling methods that facilitate detection and assignment. These methods have started to measure molecular interaction hotspots due to inherent differences in local amino acid reactivity and binding affinity throughout the proteome. Measurement of the small molecule interactome is producing structural insights and methods for probing and engineering protein biochemistry. Direct structural characterization of the small molecule interactome is a rapidly emerging area pushing new frontiers in biochemistry at the interface of small molecules and the proteome.

The Proteome Folding Project: Proteome-scale prediction of structure and function

PubMed Central

Drew, Kevin; Winters, Patrick; Butterfoss, Glenn L.; Berstis, Viktors; Uplinger, Keith; Armstrong, Jonathan; Riffle, Michael; Schweighofer, Erik; Bovermann, Bill; Goodlett, David R.; Davis, Trisha N.; Shasha, Dennis; Malmström, Lars; Bonneau, Richard

2011-01-01

The incompleteness of proteome structure and function annotation is a critical problem for biologists and, in particular, severely limits interpretation of high-throughput and next-generation experiments. We have developed a proteome annotation pipeline based on structure prediction, where function and structure annotations are generated using an integration of sequence comparison, fold recognition, and grid-computing-enabled de novo structure prediction. We predict protein domain boundaries and three-dimensional (3D) structures for protein domains from 94 genomes (including human, Arabidopsis, rice, mouse, fly, yeast, Escherichia coli, and worm). De novo structure predictions were distributed on a grid of more than 1.5 million CPUs worldwide (World Community Grid). We generated significant numbers of new confident fold annotations (9% of domains that are otherwise unannotated in these genomes). We demonstrate that predicted structures can be combined with annotations from the Gene Ontology database to predict new and more specific molecular functions. PMID:21824995

'[A]ll Our Scottish Education is in Vain': The Construction of Scottish National Identity in and by the Early Dominie Books of A. S. Neill.

ERIC Educational Resources Information Center

Limond, David

1999-01-01

Provides descriptions of two books written by Alexander Sutherland Neill: "A Dominie's Log" and "Dominie Dismissed." Considers the nature of the Dominie books as fact or fiction, looking at rhetoric and the controversy of the nature of Scottish schooling. Explores the influence Neill had on Scottish historians' writings. (CMK)

Demographic and Geographical Characteristics of Pediatric Trauma in Scotland

DTIC Science & Technology

2013-01-01

the 8-fold Scottish Urban/ Rural Classifi- cation [20], which is based on settlement size and drive time to major conurbations. Social deprivation was...distribution, but with some exceptions. Scotland has an eccentrically distributed population, with 69.5% living in urban areas ( Scottish urban/ rural ...high rate of mortality and prehospital death. Acta Anaesthesiol Scand 2003;47:153-6. [20] Scottish Government: Scottish government urban/ rural

2H and 18O Freshwater Isoscapes of Scotland

NASA Astrophysics Data System (ADS)

Meier-Augenstein, Wolfram; Hoogewerff, Jurian; Kemp, Helen; Frew, Danny

2013-04-01

Scotland's freshwater lochs and reservoirs provide a vital resource for sustaining biodiversity, agriculture, food production as well as for human consumption. Regular monitoring of freshwaters by the Scottish Environment Protection Agency (SEPA) fulfils legislative requirements with regards to water quality but new scientific methods involving stable isotope analysis present an opportunity combining these mandatory monitoring schemes with fundamental research to inform and deliver on current and nascent government policies [1] through gaining a greater understanding of Scottish waters and their importance in the context of climate change, environmental sustainability and food security. For example, 2H and 18O isoscapes of Scottish freshwater could be used to underpin research and its applications in: • Climate change - Using longitudinal changes in the characteristic isotope composition of freshwater lochs and reservoirs as proxy, isoscapes will provide a means to assess if and how changes in temperature and weather patterns might impact on precipitation patterns and amount. • Scottish branding - Location specific stable isotope signatures of Scottish freshwater have the potential to be used as a tool for provenancing and thus protecting premium Scottish produce such as Scottish beef, Scottish soft fruit and Scottish Whisky. During 2011 and 2012, with the support of SEPA more than 110 samples from freshwater lochs and reservoirs were collected from 127 different locations across Scotland including the Highlands and Islands. Here we present the results of this sampling and analysis exercise isotope analyses in form of 2H and 18O isoscapes with an unprecedented grid resolution of 26.5 × 26.5 km (or 16.4 × 16.4 miles). [1] Adaptation Framework - Adapting Our Ways: Managing Scotland's Climate Risk (2009): Scotland's Biodiversity: It's in Your Hands - A strategy for the conservation and enhancement of biodiversity in Scotland (2005); Recipe For Success - Scotland's National Food and Drink Policy (2009); Scottish Planning Policy Environmental Report (2009); Scottish Planning Policy (SPP) 15 Planning for Rural Development (2005); National Planning Policy Guideline (NPPG) 14: Natural Heritage (1999).

Negative stereotypes of the Scottish diet: A qualitative analysis of deep-fried Mars bar references in bestselling newspapers in Scotland, 2011-14.

PubMed

Knight, Christine

2016-08-01

The Scottish diet is associated in the UK media and popular discourse with unhealthy deep-fried foods. In addition to the stereotype's negative effects on perceptions of Scottish food, culture and people, there is evidence that the stereotype of the Scottish diet has negative effects on food behaviour and public health in Scotland, having been shown to encourage consumption of deep-fried foods and discourage positive dietary change. The most notorious deep-fried food associated with Scotland is the deep-fried Mars bar (DFMB), arguably invented in Stonehaven (near Aberdeen), and first reported in the Scottish and UK press in 1995. This article reports findings from an analysis of newspaper references to the DFMB in the two highest selling newspapers in Scotland, the Scottish Sun and the Daily Record, between 2011 and 2014. A keyword search ("deep fried Mars bar") using the online media database Lexis Library generated 97 unique records, and the resulting dataset was analysed thematically and discursively. Analysis showed that both newspapers clearly associated the DFMB with Scotland. Further, both newspapers portrayed the DFMB and the broader "deep-fried" Scottish diet stereotype ambivalently (mixed positive and negative associations). However, the Daily Record actively criticised the DFMB stereotype much more often than did the Scottish Sun. These findings suggest that the Scottish population encounters different messages in the press about food and nutrition from people elsewhere in the UK, and that these messages vary depending on choice of media in Scotland. Given the known negative effects of the stereotype, differences in Scottish media discourse should be considered a potential factor in persistent health inequalities affecting Scotland. Educational efforts, and opening discussion with journalists and amongst the Scottish public, may be helpful. Copyright © 2016 The Author. Published by Elsevier Ltd.. All rights reserved.

Proteomics of survival structures of fungal pathogens.

PubMed

Loginov, Dmitry; Šebela, Marek

2016-09-25

Fungal pathogens are causal agents of numerous human, animal, and plant diseases. They employ various infection modes to overcome host defense systems. Infection mechanisms of different fungi have been subjected to many comprehensive studies. These investigations have been facilitated by the development of various '-omics' techniques, and proteomics has one of the leading roles in this regard. Fungal conidia and sclerotia could be considered the most important structures for pathogenesis as their germination is one of the first steps towards a host infection. They represent interesting objects for proteomic studies because of the presence of unique proteins with unexplored biotechnological potential required for pathogen viability, development and the subsequent host infection. Proteomic peculiarities of survival structures of different fungi, including those of biotechnological significance (e.g., Asperillus fumigatus, A. nidulans, Metarhizium anisopliae), in a dormant state, as well as changes in the protein production during early stages of fungal development are the subjects of the present review. We focused on biological aspects of proteomic studies of fungal survival structures rather than on an evaluation of proteomic approaches. For that reason, proteins that have been identified in this context are discussed from the point of view of their involvement in different biological processes and possible functions assigned to them. This is the first review paper summarizing recent advances in proteomics of fungal survival structures. Copyright © 2016 Elsevier B.V. All rights reserved.

The Development of Solution Focused Multi-Agency Meetings in a Psychological Service

ERIC Educational Resources Information Center

Alexander, Shiona; Sked, Heather

2010-01-01

This article outlines the successful development of multi-agency meetings as part of a staged approach aimed at supporting families and children within the Scottish Highland Council Area. Drawing on the research evidence for the factors which help to make meetings effective, a distinctive meeting structure was developed. This structure is…

Folio Assessment or External Examinations? An Investigation into Alternative Means of Assessing SCE Ordinary Grade English. Report to the Scottish Certificate of Education Examination Board from the Scottish Council for Research in Education.

ERIC Educational Resources Information Center

Spencer, Ernest

From 1974 through 1978, three methods of assessing Scottish high school students' (O level) English achievement were studied: (1) Ordinary (O level) examinations; (2) assessment of writing skills (folio assessment); and (3) criterion referenced tests developed by the Scottish Council for Research in Education (SCRE) to measure the objectives of…

NMR in the SPINE Structural Proteomics project.

PubMed

Ab, E; Atkinson, A R; Banci, L; Bertini, I; Ciofi-Baffoni, S; Brunner, K; Diercks, T; Dötsch, V; Engelke, F; Folkers, G E; Griesinger, C; Gronwald, W; Günther, U; Habeck, M; de Jong, R N; Kalbitzer, H R; Kieffer, B; Leeflang, B R; Loss, S; Luchinat, C; Marquardsen, T; Moskau, D; Neidig, K P; Nilges, M; Piccioli, M; Pierattelli, R; Rieping, W; Schippmann, T; Schwalbe, H; Travé, G; Trenner, J; Wöhnert, J; Zweckstetter, M; Kaptein, R

2006-10-01

This paper describes the developments, role and contributions of the NMR spectroscopy groups in the Structural Proteomics In Europe (SPINE) consortium. Focusing on the development of high-throughput (HTP) pipelines for NMR structure determinations of proteins, all aspects from sample preparation, data acquisition, data processing, data analysis to structure determination have been improved with respect to sensitivity, automation, speed, robustness and validation. Specific highlights are protonless (13)C-direct detection methods and inferential structure determinations (ISD). In addition to technological improvements, these methods have been applied to deliver over 60 NMR structures of proteins, among which are five that failed to crystallize. The inclusion of NMR spectroscopy in structural proteomics pipelines improves the success rate for protein structure determinations.

Scottish Schools Science Equipment Research Centre, Bulletin No. 56, June 1972.

ERIC Educational Resources Information Center

1972

A model demonstrating the relationship between the structure of blood vessels and the flow of blood is described and illustrated in the biology section of the newsletter. The apparatus also contains a functional (but not structural) model of the heart. Suggestions for the preparation of a relatively permanent dialysis bag from visking tubing are…

Factor Structure and Reliability of the Parent-Informant Strengths and Difficulties Questionnaire in a Scottish Preschool Sample

ERIC Educational Resources Information Center

McAloney-Kocaman, Kareena; McPherson, Kerri

2017-01-01

Research Findings: Despite it being a widely accepted measure of social, emotional, and behavioral problems among children and young people, the factor structure underlying the Strengths and Difficulties Questionnaire (SDQ) is contested. Recent research has suggested a need to consider methodological bias in the SDQ, associated with the positive…

Unexpected features of the dark proteome.

PubMed

Perdigão, Nelson; Heinrich, Julian; Stolte, Christian; Sabir, Kenneth S; Buckley, Michael J; Tabor, Bruce; Signal, Beth; Gloss, Brian S; Hammang, Christopher J; Rost, Burkhard; Schafferhans, Andrea; O'Donoghue, Seán I

2015-12-29

We surveyed the "dark" proteome-that is, regions of proteins never observed by experimental structure determination and inaccessible to homology modeling. For 546,000 Swiss-Prot proteins, we found that 44-54% of the proteome in eukaryotes and viruses was dark, compared with only ∼14% in archaea and bacteria. Surprisingly, most of the dark proteome could not be accounted for by conventional explanations, such as intrinsic disorder or transmembrane regions. Nearly half of the dark proteome comprised dark proteins, in which the entire sequence lacked similarity to any known structure. Dark proteins fulfill a wide variety of functions, but a subset showed distinct and largely unexpected features, such as association with secretion, specific tissues, the endoplasmic reticulum, disulfide bonding, and proteolytic cleavage. Dark proteins also had short sequence length, low evolutionary reuse, and few known interactions with other proteins. These results suggest new research directions in structural and computational biology.

Education in the Scottish Parliament: Parliamentary Report Number 3.

ERIC Educational Resources Information Center

Donn, Gari

2000-01-01

Describes the new Scottish Parliament's first education crisis: failure of the Scottish Qualifications Authority (SQA), which oversees the public examinations system, to make timely and correct awards to secondary students who sat exams. Discusses data processing problems, accountability and ministerial responsibility, communication issues,…

ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes.

PubMed

Razban, Rostam M; Gilson, Amy I; Durfee, Niamh; Strobelt, Hendrik; Dinkla, Kasper; Choi, Jeong-Mo; Pfister, Hanspeter; Shakhnovich, Eugene I

2018-05-08

Protein evolution spans time scales and its effects span the length of an organism. A web app named ProteomeVis is developed to provide a comprehensive view of protein evolution in the S. cerevisiae and E. coli proteomes. ProteomeVis interactively creates protein chain graphs, where edges between nodes represent structure and sequence similarities within user-defined ranges, to study the long time scale effects of protein structure evolution. The short time scale effects of protein sequence evolution are studied by sequence evolutionary rate (ER) correlation analyses with protein properties that span from the molecular to the organismal level. We demonstrate the utility and versatility of ProteomeVis by investigating the distribution of edges per node in organismal protein chain universe graphs (oPCUGs) and putative ER determinants. S. cerevisiae and E. coli oPCUGs are scale-free with scaling constants of 1.79 and 1.56, respectively. Both scaling constants can be explained by a previously reported theoretical model describing protein structure evolution (Dokholyan et al., 2002). Protein abundance most strongly correlates with ER among properties in ProteomeVis, with Spearman correlations of -0.49 (p-value<10-10) and -0.46 (p-value<10-10) for S. cerevisiae and E. coli, respectively. This result is consistent with previous reports that found protein expression to be the most important ER determinant (Zhang and Yang, 2015). ProteomeVis is freely accessible at http://proteomevis.chem.harvard.edu. Supplementary data are available at Bioinformatics. shakhnovich@chemistry.harvard.edu.

Developing Inclusive Practice in Scotland: The National Framework for Inclusion

ERIC Educational Resources Information Center

Barrett, Louise; Beaton, Mhairi; Head, George; McAuliffe, Lisa; Moscardini, Lio; Spratt, Jennifer; Sutherland, Margaret

2015-01-01

This paper reports on the collaborative development of a "National Framework for Inclusion" under the auspices of the Scottish Teacher Education Committee by a working party representing each of the Scottish Universities providing initial teacher education. Recent research, international legislation and Scottish education policy have…

Social Justice Leadership in Scottish Education

ERIC Educational Resources Information Center

Torrance, Deirdre; Forde, Christine

2017-01-01

Leadership has been identified in contemporary policy as a critical factor in taking forward school improvement and enhancing outcomes for pupils (Pontz, Nusche and Moorman, 2008) in many educational systems including Scottish education. A second policy driver in Scottish education currently is focused on "closing the gap" (Scottish…

Race Equality Scheme 2005-2008

ERIC Educational Resources Information Center

Her Majesty's Inspectorate of Education, 2005

2005-01-01

Her Majesty's Inspectorate of Education (HMIE) is strongly committed to promoting race equality in the way that HMIE staff go about performing their role within Scottish education. Scottish society reflects cultural, ethnic, religious and linguistic diversity and Scottish education should be accessible to all. No-one should be disadvantaged or…

Recent developments in structural proteomics for protein structure determination.

PubMed

Liu, Hsuan-Liang; Hsu, Jyh-Ping

2005-05-01

The major challenges in structural proteomics include identifying all the proteins on the genome-wide scale, determining their structure-function relationships, and outlining the precise three-dimensional structures of the proteins. Protein structures are typically determined by experimental approaches such as X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. However, the knowledge of three-dimensional space by these techniques is still limited. Thus, computational methods such as comparative and de novo approaches and molecular dynamic simulations are intensively used as alternative tools to predict the three-dimensional structures and dynamic behavior of proteins. This review summarizes recent developments in structural proteomics for protein structure determination; including instrumental methods such as X-ray crystallography and NMR spectroscopy, and computational methods such as comparative and de novo structure prediction and molecular dynamics simulations.

Regionalism in Scottish Universities

ERIC Educational Resources Information Center

Hutchison, Dougal

1976-01-01

It is well-known that Scottish universities are highly local institutions and that over two-fifth of Scottish university students live at home. Attempts to ascertain if this regionalism has relaxed over the past twenty years with student grant regulations, improvement in communications and the increasing affluence of today's society. (Author/RK)

School Grades, School Context and University Degree Performance: Evidence from an Elite Scottish Institution

ERIC Educational Resources Information Center

Lasselle, Laurence; McDougall-Bagnall, Jonathan; Smith, Ian

2014-01-01

This paper investigates degree classification outcomes for students with SQA Higher qualifications at an elite Scottish university. Students are characterised according to a new indicator based on their secondary school's academic performance relative to the national (Scottish) average. The results show that our school context indicator provides…

Scottish Classroom Voices: A Case Study of Teaching and Learning Scots

ERIC Educational Resources Information Center

Shoba, Jo Arthur

2010-01-01

Research in multilingual classrooms demonstrates education as a key site within which social and linguistic values are shaped. This study extends such research by investigating language use in a Scottish primary classroom. Scots is widely spoken throughout Scotland, figuring in a 2003 Scottish Parliament report as one of two indigenous heritage…

Problems of Assessment in Religious and Moral Education: The Scottish Case

ERIC Educational Resources Information Center

Grant, Lynne; Matemba, Yonah H.

2013-01-01

This article is concerned with assessment issues in Religious and Moral Education (RME) offered in Scottish non-denominational schools. The analysis of the findings in this article is weighed against the framework of the new "3-18" Scottish curriculum called "Curriculum for Excellence" (CfE). CfE was introduced in primary…

Educational Theory and the Social Vision of the Scottish Enlightenment

ERIC Educational Resources Information Center

Hanley, Ryan Patrick

2011-01-01

The Scottish Enlightenment is celebrated for its many contributions to the natural sciences, the social sciences and the moral sciences. But for all this attention, one aspect of the Scottish Enlightenment has been almost entirely neglected: its educational theory. This paper aims to illuminate the relationship between the educational theory of…

Scottish outcomes for extra hepatic biliary atresia post-rationalisation of services.

PubMed

Tayler, Rachel; Barclay, Andrew R; Rogers, Pam; Mcintyre, Karen; Russell, Richard K; Devadason, David; Bisset, W Mike; Ling, Simon C; McGrogan, Paraic

2013-05-01

To evaluate the outcome of Scottish children with extra hepatic biliary atresia (EHBA) since rationalisation of Kasai services to three English centres in 2002 (The 'Group A' centres). All Scottish children with EHBA diagnosed between 2002 and 2009 were identified via the Scottish Society of Paediatric Gastroenterology, Hepatology and Nutrition (SSPGHAN) clinicians. A case-note review was conducted with demographics, presentation and outcome data recorded. These data were compared with historical Scottish data and data published previously by the supraregional liver units. 25 patients were identified, of whom 22 were referred for Kasai in the group A centres, and of whom 19 had a Kasai. 2 year transplant-free survival (TFS) was significantly lower in the SSPGHAN 2002-2009 group than the group A centres in (1) (6/18 (33%) vs 36/57 (63%), p=0.023). These postrationalisation data are disappointing. The emphasis for care will now focus on improved communication between, primary care, general paediatricians and surgical centres through regional and national managed clinical networks, aiming to improve future outcomes for Scottish children with BA.

‘We view that as contraceptive failure’: Containing the ‘multiplicity’ of contraception and abortion within Scottish reproductive healthcare

PubMed Central

Beynon-Jones, Siân M.

2013-01-01

Within contemporary Scottish policy guidance, abortion is routinely configured as evidence of a resolvable problem with the healthcare provision of contraception. This article draws on 42 semi-structured interviews with Scottish health professionals conducted during 2007–2008, in order to explore how, and in what form, realities of contraception/abortion are sustained within abortion practice. In addition to providing empirical insights concerning this sociologically neglected aspect of reproductive healthcare, it demonstrates how a novel conceptual approach could be used to develop existing social scientific analyses of the provision of techniques of fertility prevention. Science and Technology Studies (STS) has highlighted the importance of studying the complex socio-material practices through which realities are enacted (or ‘performed’). Mobilising this insight, my analysis illustrates the complex socio-material work required to enact abortion as evidence of a ‘problem’ with contraception that is resolvable within the healthcare consultation. This work, I argue, renders visible the ontologically ‘multiple’ (Mol, 2002) nature of contraception/abortion, with important implications for both social science and policy approaches to these techniques of fertility prevention. PMID:23287458

Formaldehyde cross-linking and structural proteomics: Bridging the gap.

PubMed

Srinivasa, Savita; Ding, Xuan; Kast, Juergen

2015-11-01

Proteins are dynamic entities constantly moving and altering their structures based on their functions and interactions inside and outside the cell. Formaldehyde cross-linking combined with mass spectrometry can accurately capture interactions of these rapidly changing biomolecules while maintaining their physiological surroundings. Even with its numerous established uses in biology and compatibility with mass spectrometry, formaldehyde has not yet been applied in structural proteomics. However, formaldehyde cross-linking is moving toward analyzing tertiary structure, which conventional cross-linkers have already accomplished. The purpose of this review is to describe the potential of formaldehyde cross-linking in structural proteomics by highlighting its applications, characteristics and current status in the field. Copyright © 2015 Elsevier Inc. All rights reserved.

Functional insights from proteome-wide structural modeling of Treponema pallidum subspecies pallidum, the causative agent of syphilis.

PubMed

Houston, Simon; Lithgow, Karen Vivien; Osbak, Kara Krista; Kenyon, Chris Richard; Cameron, Caroline E

2018-05-16

Syphilis continues to be a major global health threat with 11 million new infections each year, and a global burden of 36 million cases. The causative agent of syphilis, Treponema pallidum subspecies pallidum, is a highly virulent bacterium, however the molecular mechanisms underlying T. pallidum pathogenesis remain to be definitively identified. This is due to the fact that T. pallidum is currently uncultivatable, inherently fragile and thus difficult to work with, and phylogenetically distinct with no conventional virulence factor homologs found in other pathogens. In fact, approximately 30% of its predicted protein-coding genes have no known orthologs or assigned functions. Here we employed a structural bioinformatics approach using Phyre2-based tertiary structure modeling to improve our understanding of T. pallidum protein function on a proteome-wide scale. Phyre2-based tertiary structure modeling generated high-confidence predictions for 80% of the T. pallidum proteome (780/978 predicted proteins). Tertiary structure modeling also inferred the same function as primary structure-based annotations from genome sequencing pipelines for 525/605 proteins (87%), which represents 54% (525/978) of all T. pallidum proteins. Of the 175 T. pallidum proteins modeled with high confidence that were not assigned functions in the previously annotated published proteome, 167 (95%) were able to be assigned predicted functions. Twenty-one of the 175 hypothetical proteins modeled with high confidence were also predicted to exhibit significant structural similarity with proteins experimentally confirmed to be required for virulence in other pathogens. Phyre2-based structural modeling is a powerful bioinformatics tool that has provided insight into the potential structure and function of the majority of T. pallidum proteins and helped validate the primary structure-based annotation of more than 50% of all T. pallidum proteins with high confidence. This work represents the first T. pallidum proteome-wide structural modeling study and is one of few studies to apply this approach for the functional annotation of a whole proteome.

Enhancing Bottom-up and Top-down Proteomic Measurements with Ion Mobility Separations

DOE PAGES

Baker, Erin Shammel; Burnum-Johnson, Kristin E.; Ibrahim, Yehia M.; ...

2015-07-03

Proteomic measurements with greater throughput, sensitivity and additional structural information enhance the in-depth characterization of complex mixtures and targeted studies with additional information and higher confidence. While liquid chromatography separation coupled with mass spectrometry (LC-MS) measurements have provided information on thousands of proteins in different sample types, the additional of another rapid separation stage providing structural information has many benefits for analyses. Technical advances in ion funnels and multiplexing have enabled ion mobility separations to be easily and effectively coupled with LC-MS proteomics to enhance the information content of measurements. Finally, herein, we report on applications illustrating increased sensitivity, throughput,more » and structural information by utilizing IMS-MS and LC-IMS-MS measurements for both bottom-up and top-down proteomics measurements.« less

Teaching China in Scotland's Secondary Schools as Sino-Scottish Engagement Intensifies

ERIC Educational Resources Information Center

Oates, John Vincent

2011-01-01

At a time of burgeoning Sino-Scottish engagement, and the introduction of a new national education policy, "Curriculum for Excellence" designed to enhance teacher autonomy, this paper draws on the national response of Modern Studies teachers who are the only group of Scottish teachers to have the (voluntary) option of including the study…

English--Personal Growth and Public Accountability: The Scottish Experience.

ERIC Educational Resources Information Center

Northcroft, David J.

The implementation of a set of curriculum standards in Scottish public schools has raised some fears among Scottish teachers of English over whether such strict guidelines will impede the use of literary education to foster students' personal growth. Previously, freed from many curricular restrictions by a series of reforms in the 1960s and 1970s,…

Nurture Groups in a Scottish Secondary School: Purpose, Features, Value and Areas for Development

ERIC Educational Resources Information Center

Kourmoulaki, Athina

2013-01-01

Nurture groups (NGs) are increasingly being established in Scottish secondary schools yet research in this context is limited. The current study explores the purpose, features and value of two NGs in a Scottish secondary school through interviewing current and former NG members, parents/carers, NG staff and other school staff. A thematic analysis…

Seven Years of Linking Scottish Schools and Industry with SSTN

ERIC Educational Resources Information Center

Whittington, Gary; Lowson, Sandra

2007-01-01

The Scottish Science and Technology Network (SSTN) is a major collaboration between Careers Scotland and Scottish industry to promote science and technology via an on-line and integrated learning programme. An initial two-year pilot project has grown considerably and has now been running for over 7 years. The SSTN programme is a web-based…

The Impact of ICT Initiatives in Scottish Schools: Cultural Issues.

ERIC Educational Resources Information Center

Condie, Rae; Simpson, Mary

2004-01-01

At the beginning of a series of ICT (information and communication technology) initiatives in Scottish schools by the Scottish Executive and again, 2 years later, a survey of teachers and pupils provided evidence of the impact that these strategic investments had made on the classroom. The findings indicate that while there are innovative and…

High-resolution proteomic profiling of spider venom: expanding the toxin diversity of Phoneutria nigriventer venom.

PubMed

Liberato, Tarcísio; Troncone, Lanfranco Ranieri Paolo; Yamashiro, Edson T; Serrano, Solange M T; Zelanis, André

2016-03-01

Here we present a proteomic characterization of Phoneutria nigriventer venom. A shotgun proteomic approach allowed the identification, for the first time, of O-glycosyl hydrolases (chitinases) in P. nigriventer venom. The electrophoretic profiles under nonreducing and reducing conditions, and protein identification by mass spectrometry, indicated the presence of oligomeric toxin structures in the venom. Complementary proteomic approaches allowed for a qualitative and semi-quantitative profiling of P. nigriventer venom complexity, expanding its known venom proteome diversity.

Embodied intersubjective engagement in mother–infant tactile communication: a cross-cultural study of Japanese and Scottish mother–infant behaviors during infant pick-up

PubMed Central

Negayama, Koichi; Delafield-Butt, Jonathan T.; Momose, Keiko; Ishijima, Konomi; Kawahara, Noriko; Lux, Erin J.; Murphy, Andrew; Kaliarntas, Konstantinos

2015-01-01

This study examines the early development of cultural differences in a simple, embodied, and intersubjective engagement between mothers putting down, picking up, and carrying their infants between Japan and Scotland. Eleven Japanese and ten Scottish mothers with their 6- and then 9-month-old infants participated. Video and motion analyses were employed to measure motor patterns of the mothers’ approach to their infants, as well as their infants’ collaborative responses during put-down, pick-up, and carry phases. Japanese and Scottish mothers approached their infants with different styles and their infants responded differently to the short duration of separation during the trial. A greeting-like behavior of the arms and hands was prevalent in the Scottish mothers’ approach, but not in the Japanese mothers’ approach. Japanese mothers typically kneeled before making the final reach to pick-up their children, giving a closer, apparently gentler final approach of the torso than Scottish mothers, who bent at the waist with larger movements of the torso. Measures of the gap closure between the mothers’ hands to their infants’ heads revealed variably longer duration and distance gap closures with greater velocity by the Scottish mothers than by the Japanese mothers. Further, the sequence of Japanese mothers’ body actions on approach, contact, pick-up, and hold was more coordinated at 6 months than at 9 months. Scottish mothers were generally more variable on approach. Measures of infant participation and expressivity indicate more active participation in the negotiation during the separation and pick-up phases by Scottish infants. Thus, this paper demonstrates a culturally different onset of development of joint attention in pick-up. These differences reflect cultures of everyday interaction. PMID:25774139

Embodied intersubjective engagement in mother-infant tactile communication: a cross-cultural study of Japanese and Scottish mother-infant behaviors during infant pick-up.

PubMed

Negayama, Koichi; Delafield-Butt, Jonathan T; Momose, Keiko; Ishijima, Konomi; Kawahara, Noriko; Lux, Erin J; Murphy, Andrew; Kaliarntas, Konstantinos

2015-01-01

This study examines the early development of cultural differences in a simple, embodied, and intersubjective engagement between mothers putting down, picking up, and carrying their infants between Japan and Scotland. Eleven Japanese and ten Scottish mothers with their 6- and then 9-month-old infants participated. Video and motion analyses were employed to measure motor patterns of the mothers' approach to their infants, as well as their infants' collaborative responses during put-down, pick-up, and carry phases. Japanese and Scottish mothers approached their infants with different styles and their infants responded differently to the short duration of separation during the trial. A greeting-like behavior of the arms and hands was prevalent in the Scottish mothers' approach, but not in the Japanese mothers' approach. Japanese mothers typically kneeled before making the final reach to pick-up their children, giving a closer, apparently gentler final approach of the torso than Scottish mothers, who bent at the waist with larger movements of the torso. Measures of the gap closure between the mothers' hands to their infants' heads revealed variably longer duration and distance gap closures with greater velocity by the Scottish mothers than by the Japanese mothers. Further, the sequence of Japanese mothers' body actions on approach, contact, pick-up, and hold was more coordinated at 6 months than at 9 months. Scottish mothers were generally more variable on approach. Measures of infant participation and expressivity indicate more active participation in the negotiation during the separation and pick-up phases by Scottish infants. Thus, this paper demonstrates a culturally different onset of development of joint attention in pick-up. These differences reflect cultures of everyday interaction.

Mutuality in the provision of Scottish healthcare.

PubMed

Howieson, Brian

2015-11-01

The backdrop to this article is provided by the Better Health, Better Care Action Plan (Scottish Government, 2007), Section 1 of which is entitled 'Towards a Mutual NHS'. According to Better Health, Better Care (Scottish Government, 2007: 5): 'Mutual organisations are designed to serve their members. They are designed to gather people around a common sense of purpose. They are designed to bring the organisation together in what people often call "co-production."' The aim of this article is to précis the current knowledge of mutuality in the provision of Scottish healthcare. In detail, it will: introduce the 'mutual' organisation; offer a historical perspective of mutuality; suggest why healthcare mutuality is important; and briefly, detail the differences in mutual health-care policy in England and Scotland. It is hoped that this analysis will help researchers and practitioners alike appreciate further the philosophy of mutuality in the provision of Scottish healthcare. © The Author(s) 2015.

One World, Many Cultures. Papers from the International Conference on Adult Education and the Arts (4th, St. Andrews, Scotland, July 10-14, 1995).

ERIC Educational Resources Information Center

Jones, David, Ed.; McConnell, Bridget, Ed.; Normie, Gerald, Ed.

The following papers are included: "Foreword" (Bridget McConnell); "Introduction" (David J. Jones); opening addresses by George Robertson MP, Shadow Scottish Secretary, and by Charlie McConnell, Executive Director, Scottish Community Education Council; and speech by Christine Hamilton, Deputy Director, Scottish Arts Council;…

Is there a 'Scottish effect' for mortality? Prospective observational study of census linkage studies.

PubMed

Popham, Frank; Boyle, Paul J

2011-09-01

Scotland's mortality rate is higher than England and Wales' and this difference cannot be explained by differences in area-level socio-economic deprivation. However, studies of this 'Scottish effect' have not adjusted for individual-level measures of socio-economic position nor accounted for country of birth; important as Scottish born living in England and Wales also have high mortality risk. Data sets (1991-2001 and 2001-2007) were obtained from the Scottish Longitudinal Study and the Office for National Statistics England and Wales Longitudinal Study that both link census records to subsequent mortality. Analysis was limited to those aged 35-74 at baseline with people followed to emigration, death or end of follow-up. Those born in Scotland living in either England and Wales or Scotland had a higher mortality rate than the English born living in England and Wales that was not fully attenuated by adjustment for car access and housing tenure. Adjusting for household-level differences in socio-economic deprivation does not fully explain the Scottish excess mortality that is seen for those born in Scotland whether living in England and Wales or Scotland. Taking a life course approach may reveal the cause of the 'Scottish effect'.

Variation in practice: an analysis of Scottish Surgical Profiles ENT data.

PubMed

Yeo, J C L; Ah-See, K W; Mackenzie, K

2013-02-01

Variation in otolaryngology intervention rates is reported in the Scottish Surgical Profiles Project. Tonsillectomy is one of the selected key indicator procedures. The variation in practice was discussed nationally at the Scottish Otolaryngology Society summer meetings in 2009 and 2010. NHS Grampian had a significantly higher tonsillectomy rate compared with other Scottish NHS boards. To determine the accuracy of NHS Grampian data reported by the Information Service Division (ISD) and to record the appropriateness of listing of patients for tonsillectomy with reference to the Scottish Intercollegiate Guidelines Network (SIGN). Retrospective review of case notes and surgical records of patients who had undergone tonsillectomy between March 2007 and March 2008 in NHS Grampian. Between March 2007 and March 2008, 509 tonsillectomy cases were performed in NHS Grampian. This corresponded to the data received from ISD. 87% of tonsillectomies performed were compliant with SIGN guidelines. The Scottish otolaryngology clinicians have found the reporting of the intervention rates stimulating and challenging. Discussion of the surgical profile project regularly at national specialty meetings resulted in a preliminary detailed targeted audit of those who were persistent outliers for tonsillectomy. This refuted the presumed reasons for this variation, namely inaccurate figures from ISD and inappropriate listings by clinicians.

DEFINING THE MANDATE OF PROTEOMICS IN THE POST-GENOMIC ERA: WORKSHOP REPORT

EPA Science Inventory

Research in proteomics is the next step after genomics in understanding life processes at the molecular level. In the largest sense proteomics encompasses knowledge of the structure, function and expression of all proteins in the biochemical or biological contexts of all organism...

The Redox Proteome*

PubMed Central

Go, Young-Mi; Jones, Dean P.

2013-01-01

The redox proteome consists of reversible and irreversible covalent modifications that link redox metabolism to biologic structure and function. These modifications, especially of Cys, function at the molecular level in protein folding and maturation, catalytic activity, signaling, and macromolecular interactions and at the macroscopic level in control of secretion and cell shape. Interaction of the redox proteome with redox-active chemicals is central to macromolecular structure, regulation, and signaling during the life cycle and has a central role in the tolerance and adaptability to diet and environmental challenges. PMID:23861437

Multiclassifier combinatorial proteomics of organelle shadows at the example of mitochondria in chromatin data.

PubMed

Kustatscher, Georg; Grabowski, Piotr; Rappsilber, Juri

2016-02-01

Subcellular localization is an important aspect of protein function, but the protein composition of many intracellular compartments is poorly characterized. For example, many nuclear bodies are challenging to isolate biochemically and thus remain inaccessible to proteomics. Here, we explore covariation in proteomics data as an alternative route to subcellular proteomes. Rather than targeting a structure of interest biochemically, we target it by machine learning. This becomes possible by taking data obtained for one organelle and searching it for traces of another organelle. As an extreme example and proof-of-concept we predict mitochondrial proteins based on their covariation in published interphase chromatin data. We detect about ⅓ of the known mitochondrial proteins in our chromatin data, presumably most as contaminants. However, these proteins are not present at random. We show covariation of mitochondrial proteins in chromatin proteomics data. We then exploit this covariation by multiclassifier combinatorial proteomics to define a list of mitochondrial proteins. This list agrees well with different databases on mitochondrial composition. This benchmark test raises the possibility that, in principle, covariation proteomics may also be applicable to structures for which no biochemical isolation procedures are available. © 2015 The Authors. Proteomics Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Local Authority Education in a Democratic Scotland.

ERIC Educational Resources Information Center

Fairley, John

1998-01-01

Establishment of a Scottish Parliament in 1999 will pose questions about its relationship to local authorities and their role in education. Possible scenarios are discussed in which Parliament pursues centralization or decentralization in education policy. Recent reforms to local government structures may allow local councils to become partners of…

Experiences and Outcomes of Preschool Physical Education: An Analysis of Developmental Discourses in Scottish Curricular Documentation

ERIC Educational Resources Information Center

McEvilly, Nollaig

2014-01-01

This article provides an analysis of developmental discourses underpinning preschool physical education in Scotland's Curriculum for Excellence. Implementing a post-structural perspective, the article examines the preschool experiences and outcomes related to physical education as presented in the Curriculum for Excellence "health and…

CPD: Support Strategies for Professional Learning, National Initiatives and Major Curriculum Reform

ERIC Educational Resources Information Center

Cumming, Carol

2011-01-01

This article outlines developments in continuous professional development (CPD) for teachers, within the Scottish context. It discusses some examples of both bottom-up and top-down structures, approaches to, and opportunities for CPD within Scotland, contextualizing the importance of professional learning within global issues of educational…

Adolescent Drinking Behaviour and the Role of Family Life: A Scottish Perspective.

ERIC Educational Resources Information Center

Shucksmith, Janet; Glendinning, Anthony; Hendry, Leo

1997-01-01

Explores young people's alcohol consumption with respect to their families' social position and patterns of support and control by parents. Longitudinal analysis of over 600 participants indicate that family structure influenced young persons' alcohol use, but drinking behavior was unrelated to the families' socioeconomic circumstances. Other…

Democracy and power in alcohol premises licensing: A qualitative interview study of the Scottish public health objective.

PubMed

Fitzgerald, Niamh; Winterbottom, Jo; Nicholls, James

2018-06-11

There is international interest in how the availability of alcohol can be controlled to reduce harms. An objective of 'protecting and improving public health' was introduced to alcohol premises licensing in Scotland in 2005, resulting in public health actors engaging with licensing in new ways. We aimed to explore their experiences, including perceptions of the distribution of power, and constraints on their influence and that of the general public within the licensing system. In-depth, semi-structured interviews were conducted with 13 public health actors who had recent and extensive experience of involvement in local licensing in 20 Scottish licensing jurisdictions. Interviews were audio-recorded and analysed using an inductive framework approach. Public health actors reported experiencing the licensing process as inherently unfair, with structures and traditions that were largely unhelpful to their efforts to support the public health objective. These included influence exerted by local officials, the formal and quasi-judicial conduct of licensing meetings, and the disparity in resources available to public health actors versus licence applicants-with many larger applicants engaging specialist lawyers to represent their interests. The influence of public opinion-through, for instance, elected representatives' perceptions of public attitudes, consultation exercises and local 'licensing forums'-was seen as having a limited effect on decision-making. Changes to Scottish alcohol licensing ostensibly designed to enhance democratic engagement and promote public health, were as yet insufficient to change the system, or empower stakeholders, to fully achieve those goals. © 2018 Australasian Professional Society on Alcohol and other Drugs.

Childhood IQ and In-Service Mortality in Scottish Army Personnel during World War II

ERIC Educational Resources Information Center

Corley, Janie; Crang, Jeremy A.; Deary, Ian J.

2009-01-01

The Scottish Mental Survey of 1932 (SMS1932) provides a record of intelligence test scores for almost a complete year-of-birth group of children born in 1921. By linking UK Army personnel records, the Scottish National War Memorial data, and the SMS1932 dataset it was possible to examine the effect of childhood intelligence scores on wartime…

An integrated native mass spectrometry and top-down proteomics method that connects sequence to structure and function of macromolecular complexes

NASA Astrophysics Data System (ADS)

Li, Huilin; Nguyen, Hong Hanh; Ogorzalek Loo, Rachel R.; Campuzano, Iain D. G.; Loo, Joseph A.

2018-02-01

Mass spectrometry (MS) has become a crucial technique for the analysis of protein complexes. Native MS has traditionally examined protein subunit arrangements, while proteomics MS has focused on sequence identification. These two techniques are usually performed separately without taking advantage of the synergies between them. Here we describe the development of an integrated native MS and top-down proteomics method using Fourier-transform ion cyclotron resonance (FTICR) to analyse macromolecular protein complexes in a single experiment. We address previous concerns of employing FTICR MS to measure large macromolecular complexes by demonstrating the detection of complexes up to 1.8 MDa, and we demonstrate the efficacy of this technique for direct acquirement of sequence to higher-order structural information with several large complexes. We then summarize the unique functionalities of different activation/dissociation techniques. The platform expands the ability of MS to integrate proteomics and structural biology to provide insights into protein structure, function and regulation.

Concurrent Transitional Meningioma and Ceruminous Gland Adenocarcinoma in a Scottish Wildcat Hybrid (Felis silvestris).

PubMed

Drew, S J; Perpiñán, D; Baily, J

2016-01-01

The Scottish wildcat (Felis silvestris) is an iconic and endangered subpopulation of the European wildcat (F. silvestris silvestris). There is much research devoted to the ecology, genetics and conservation of this animal, but little published information on pathology and disease. The investigation and reporting of such information is vital to furthering understanding of the effects of hybridization, a factor that is crucial if we are to secure a future for the Scottish wildcat. This report describes the clinical presentation, gross post-mortem and histological findings in an elderly Scottish wildcat hybrid with concurrent transitional meningioma and ceruminous gland adenocarcinoma. Copyright © 2015 Elsevier Ltd. All rights reserved.

Proteomic analysis of bovine nucleolus.

PubMed

Patel, Amrutlal K; Olson, Doug; Tikoo, Suresh K

2010-09-01

Nucleolus is the most prominent subnuclear structure, which performs a wide variety of functions in the eukaryotic cellular processes. In order to understand the structural and functional role of the nucleoli in bovine cells, we analyzed the proteomic composition of the bovine nucleoli. The nucleoli were isolated from Madin Darby bovine kidney cells and subjected to proteomic analysis by LC-MS/MS after fractionation by SDS-PAGE and strong cation exchange chromatography. Analysis of the data using the Mascot database search and the GPM database search identified 311 proteins in the bovine nucleoli, which contained 22 proteins previously not identified in the proteomic analysis of human nucleoli. Analysis of the identified proteins using the GoMiner software suggested that the bovine nucleoli contained proteins involved in ribosomal biogenesis, cell cycle control, transcriptional, translational and post-translational regulation, transport, and structural organization. Copyright © 2010 Beijing Genomics Institute. Published by Elsevier Ltd. All rights reserved.

Unexpected features of the dark proteome

PubMed Central

Perdigão, Nelson; Heinrich, Julian; Stolte, Christian; Sabir, Kenneth S.; Buckley, Michael J.; Tabor, Bruce; Signal, Beth; Gloss, Brian S.; Hammang, Christopher J.; Rost, Burkhard; Schafferhans, Andrea

2015-01-01

We surveyed the “dark” proteome–that is, regions of proteins never observed by experimental structure determination and inaccessible to homology modeling. For 546,000 Swiss-Prot proteins, we found that 44–54% of the proteome in eukaryotes and viruses was dark, compared with only ∼14% in archaea and bacteria. Surprisingly, most of the dark proteome could not be accounted for by conventional explanations, such as intrinsic disorder or transmembrane regions. Nearly half of the dark proteome comprised dark proteins, in which the entire sequence lacked similarity to any known structure. Dark proteins fulfill a wide variety of functions, but a subset showed distinct and largely unexpected features, such as association with secretion, specific tissues, the endoplasmic reticulum, disulfide bonding, and proteolytic cleavage. Dark proteins also had short sequence length, low evolutionary reuse, and few known interactions with other proteins. These results suggest new research directions in structural and computational biology. PMID:26578815

Application of the multidimensional fatigue inventory (MFI-20) in cancer patients receiving radiotherapy.

PubMed Central

Smets, E. M.; Garssen, B.; Cull, A.; de Haes, J. C.

1996-01-01

In this paper the psychometric properties of the multidimensional fatigue inventory (MFI-20) are established further in cancer patients. The MFI is a 20-item self-report instrument designed to measure fatigue. It covers the following dimensions: general fatigue, physical fatigue, reduced activity, reduced motivation and mental fatigue. The instrument was used in a Dutch and Scottish sample of cancer patients receiving radiotherapy. The dimensional structure was assessed using confirmatory factor analyses (Lisrel's unweighted least-squares method). The hypothesised five-factor model appeared to fit the data in both samples (adjusted goodness of fit; AGFI: 0.97 and 0.98). Internal consistency of the separate scales was good in both the Dutch and Scottish samples with Cronbach's alpha coefficients ranging from 0.79 to 0.93. Construct validity was assessed by correlating the MFI-20 to activities of daily living, anxiety and depression. Significant relations were assumed. Convergent validity was investigated by correlating the MFI scales with a visual analogue scale measuring fatigue and with a fatigue-scale derived from the Rotterdam Symptom Checklist. Results support the validity of the MFI-20. The highly similar results in the Dutch and Scottish sample suggest that the portrayal of fatigue using the MFI-20 is quite robust. PMID:8546913

Review of the Contribution of the Scottish Science Centres Network to Formal and Informal Science Education: Report of Follow-Through Visits by HM Inspectorate of Education--June 2009

ERIC Educational Resources Information Center

Her Majesty's Inspectorate of Education, 2009

2009-01-01

In 2006, the Scottish Executive's Enterprise, Transport and Lifelong Learning Department (SEETLLD) asked HM Inspectorate of Education (HMIE) to carry out a review of the four Scottish science centres--Glasgow Science Centre (GSC), Our Dynamic Earth (ODE) in Edinburgh, Satrosphere Science Centre in Aberdeen, and Sensation Science Centre in Dundee.…

Attitudes of Scottish abortion care providers towards provision of abortion after 16 weeks' gestation within Scotland.

PubMed

Cochrane, Rosemary A; Cameron, Sharon T

2013-06-01

In Scotland, in contrast to the rest of Great Britain, abortion at gestations over 20 weeks is not provided, and provision of procedures above 16 weeks varies considerably between regions. Women at varying gestations above 16 weeks must travel outside Scotland, usually to England, for the procedure. To determine the views of professionals working within Scottish abortion care about a Scottish late abortion service. Delegates at a meeting for abortion providers in Scotland completed a questionnaire about their views on abortion provision over 16 weeks and their perceived barriers to service provision. Of 95 distributed questionnaires, 70 (76%) were analysed. Fifty-six respondents (80%) supported a Scottish late abortion service, ten (14%) would maintain current service arrangements, and five (7%) were undecided. Forty (57%) of the supporters of a Scottish service would prefer a single national service, and 16 (22%) several regional services. Perceived barriers included lack of trained staff (n = 39; 56%), accommodation for the service (n = 34; 48%), and perception of lack of support among senior management (n = 28; 40%). The majority of health professionals surveyed who work in Scottish abortion services support provision of abortion beyond 16 weeks within Scotland, and most favour a single national service. Further work on the feasibility of providing this service is required.

Cross-Cultural Agreement in Facial Attractiveness Preferences: The Role of Ethnicity and Gender

PubMed Central

Coetzee, Vinet; Greeff, Jaco M.; Stephen, Ian D.; Perrett, David I.

2014-01-01

Previous work showed high agreement in facial attractiveness preferences within and across cultures. The aims of the current study were twofold. First, we tested cross-cultural agreement in the attractiveness judgements of White Scottish and Black South African students for own- and other-ethnicity faces. Results showed significant agreement between White Scottish and Black South African observers' attractiveness judgements, providing further evidence of strong cross-cultural agreement in facial attractiveness preferences. Second, we tested whether cross-cultural agreement is influenced by the ethnicity and/or the gender of the target group. White Scottish and Black South African observers showed significantly higher agreement for Scottish than for African faces, presumably because both groups are familiar with White European facial features, but the Scottish group are less familiar with Black African facial features. Further work investigating this discordance in cross-cultural attractiveness preferences for African faces show that Black South African observers rely more heavily on colour cues when judging African female faces for attractiveness, while White Scottish observers rely more heavily on shape cues. Results also show higher cross-cultural agreement for female, compared to male faces, albeit not significantly higher. The findings shed new light on the factors that influence cross-cultural agreement in attractiveness preferences. PMID:24988325

A historical review of the key bacterial and viral pathogens of Scottish wild fish.

PubMed

Wallace, I S; McKay, P; Murray, A G

2017-12-01

Thousands of Scottish wild fish were screened for pathogens by Marine Scotland Science. A systematic review of published and unpublished data on six key pathogens (Renibacterium salmoninarum, Aeromonas salmonicida, IPNV, ISAV, SAV and VHSV) found in Scottish wild and farmed fish was undertaken. Despite many reported cases in farmed fish, there was a limited number of positive samples from Scottish wild fish, however, there was evidence for interactions between wild and farmed fish. A slightly elevated IPNV prevalence was reported in wild marine fish caught close to Atlantic salmon, Salmo salar L., farms that had undergone clinical IPN. Salmonid alphavirus was isolated from wild marine fish caught near Atlantic salmon farms with a SAV infection history. Isolations of VHSV were made from cleaner wrasse (Labridae) used on Scottish Atlantic salmon farms and VHSV was detected in local wild marine fish. However, these pathogens have been detected in wild marine fish caught remotely from aquaculture sites. These data suggest that despite the large number of samples taken, there is limited evidence for clinical disease in wild fish due to these pathogens (although BKD and furunculosis historically occurred) and they are likely to have had a minimal impact on Scottish wild fish. © 2017 Crown Copyright. Journal of Fish Diseases © 2017 John Wiley & Sons Ltd.

Cross-cultural agreement in facial attractiveness preferences: the role of ethnicity and gender.

PubMed

Coetzee, Vinet; Greeff, Jaco M; Stephen, Ian D; Perrett, David I

2014-01-01

Previous work showed high agreement in facial attractiveness preferences within and across cultures. The aims of the current study were twofold. First, we tested cross-cultural agreement in the attractiveness judgements of White Scottish and Black South African students for own- and other-ethnicity faces. Results showed significant agreement between White Scottish and Black South African observers' attractiveness judgements, providing further evidence of strong cross-cultural agreement in facial attractiveness preferences. Second, we tested whether cross-cultural agreement is influenced by the ethnicity and/or the gender of the target group. White Scottish and Black South African observers showed significantly higher agreement for Scottish than for African faces, presumably because both groups are familiar with White European facial features, but the Scottish group are less familiar with Black African facial features. Further work investigating this discordance in cross-cultural attractiveness preferences for African faces show that Black South African observers rely more heavily on colour cues when judging African female faces for attractiveness, while White Scottish observers rely more heavily on shape cues. Results also show higher cross-cultural agreement for female, compared to male faces, albeit not significantly higher. The findings shed new light on the factors that influence cross-cultural agreement in attractiveness preferences.

High throughput profile-profile based fold recognition for the entire human proteome.

PubMed

McGuffin, Liam J; Smith, Richard T; Bryson, Kevin; Sørensen, Søren-Aksel; Jones, David T

2006-06-07

In order to maintain the most comprehensive structural annotation databases we must carry out regular updates for each proteome using the latest profile-profile fold recognition methods. The ability to carry out these updates on demand is necessary to keep pace with the regular updates of sequence and structure databases. Providing the highest quality structural models requires the most intensive profile-profile fold recognition methods running with the very latest available sequence databases and fold libraries. However, running these methods on such a regular basis for every sequenced proteome requires large amounts of processing power. In this paper we describe and benchmark the JYDE (Job Yield Distribution Environment) system, which is a meta-scheduler designed to work above cluster schedulers, such as Sun Grid Engine (SGE) or Condor. We demonstrate the ability of JYDE to distribute the load of genomic-scale fold recognition across multiple independent Grid domains. We use the most recent profile-profile version of our mGenTHREADER software in order to annotate the latest version of the Human proteome against the latest sequence and structure databases in as short a time as possible. We show that our JYDE system is able to scale to large numbers of intensive fold recognition jobs running across several independent computer clusters. Using our JYDE system we have been able to annotate 99.9% of the protein sequences within the Human proteome in less than 24 hours, by harnessing over 500 CPUs from 3 independent Grid domains. This study clearly demonstrates the feasibility of carrying out on demand high quality structural annotations for the proteomes of major eukaryotic organisms. Specifically, we have shown that it is now possible to provide complete regular updates of profile-profile based fold recognition models for entire eukaryotic proteomes, through the use of Grid middleware such as JYDE.

Structural bioinformatics of the human spliceosomal proteome

PubMed Central

Korneta, Iga; Magnus, Marcin; Bujnicki, Janusz M.

2012-01-01

In this work, we describe the results of a comprehensive structural bioinformatics analysis of the spliceosomal proteome. We used fold recognition analysis to complement prior data on the ordered domains of 252 human splicing proteins. Examples of newly identified domains include a PWI domain in the U5 snRNP protein 200K (hBrr2, residues 258–338), while examples of previously known domains with a newly determined fold include the DUF1115 domain of the U4/U6 di-snRNP protein 90K (hPrp3, residues 540–683). We also established a non-redundant set of experimental models of spliceosomal proteins, as well as constructed in silico models for regions without an experimental structure. The combined set of structural models is available for download. Altogether, over 90% of the ordered regions of the spliceosomal proteome can be represented structurally with a high degree of confidence. We analyzed the reduced spliceosomal proteome of the intron-poor organism Giardia lamblia, and as a result, we proposed a candidate set of ordered structural regions necessary for a functional spliceosome. The results of this work will aid experimental and structural analyses of the spliceosomal proteins and complexes, and can serve as a starting point for multiscale modeling of the structure of the entire spliceosome. PMID:22573172

Seven perspectives on GPCR H/D-exchange proteomics methods

PubMed Central

Zhang, Xi

2017-01-01

Recent research shows surging interest to visualize human G protein-coupled receptor (GPCR) dynamic structures using the bottom-up H/D-exchange (HDX) proteomics technology. This opinion article clarifies critical technical nuances and logical thinking behind the GPCR HDX proteomics method, to help scientists overcome cross-discipline pitfalls, and understand and reproduce the protocol at high quality. The 2010 89% HDX structural coverage of GPCR was achieved with both structural and analytical rigor. This article emphasizes systematically considering membrane protein structure stability and compatibility with chromatography and mass spectrometry (MS) throughout the pipeline, including the effects of metal ions, zero-detergent shock, and freeze-thaws on HDX result rigor. This article proposes to view bottom-up HDX as two steps to guide choices of detergent buffers and chromatography settings: (I) protein HDX labeling in native buffers, and (II) peptide-centric analysis of HDX labels, which applies (a) bottom-up MS/MS to construct peptide matrix and (b) HDX MS to locate and quantify H/D labels. The detergent-low-TCEP digestion method demystified the challenge of HDX-grade GPCR digestion. GPCR HDX proteomics is a structural approach, thus its choice of experimental conditions should let structure lead and digestion follow, not the opposite. PMID:28529698

Proteomic approaches in research of cyanobacterial photosynthesis.

PubMed

Battchikova, Natalia; Angeleri, Martina; Aro, Eva-Mari

2015-10-01

Oxygenic photosynthesis in cyanobacteria, algae, and plants is carried out by a fabulous pigment-protein machinery that is amazingly complicated in structure and function. Many different approaches have been undertaken to characterize the most important aspects of photosynthesis, and proteomics has become the essential component in this research. Here we describe various methods which have been used in proteomic research of cyanobacteria, and demonstrate how proteomics is implemented into on-going studies of photosynthesis in cyanobacterial cells.

Proteome complexity and the forces that drive proteome imbalance.

PubMed

Harper, J Wade; Bennett, Eric J

2016-09-15

The cellular proteome is a complex microcosm of structural and regulatory networks that requires continuous surveillance and modification to meet the dynamic needs of the cell. It is therefore crucial that the protein flux of the cell remains in balance to ensure proper cell function. Genetic alterations that range from chromosome imbalance to oncogene activation can affect the speed, fidelity and capacity of protein biogenesis and degradation systems, which often results in proteome imbalance. An improved understanding of the causes and consequences of proteome imbalance is helping to reveal how these systems can be targeted to treat diseases such as cancer.

Phylogenetic Tracings of Proteome Size Support the Gradual Accretion of Protein Structural Domains and the Early Origin of Viruses from Primordial Cells

PubMed Central

Nasir, Arshan; Kim, Kyung Mo; Caetano-Anollés, Gustavo

2017-01-01

Untangling the origin and evolution of viruses remains a challenging proposition. We recently studied the global distribution of protein domain structures in thousands of completely sequenced viral and cellular proteomes with comparative genomics, phylogenomics, and multidimensional scaling methods. A tree of life describing the evolution of proteomes revealed viruses emerging from the base of the tree as a fourth supergroup of life. A tree of domains indicated an early origin of modern viral lineages from ancient cells that co-existed with the cellular ancestors. However, it was recently argued that the rooting of our trees and the basal placement of viruses was artifactually induced by small genome (proteome) size. Here we show that these claims arise from misunderstanding and misinterpretations of cladistic methodology. Trees are reconstructed unrooted, and thus, their topologies cannot be distorted a posteriori by the rooting methodology. Tracing proteome size in trees and multidimensional views of evolutionary relationships as well as tests of leaf stability and exclusion/inclusion of taxa demonstrated that the smallest proteomes were neither attracted toward the root nor caused any topological distortions of the trees. Simulations confirmed that taxa clustering patterns were independent of proteome size and were determined by the presence of known evolutionary relatives in data matrices, highlighting the need for broader taxon sampling in phylogeny reconstruction. Instead, phylogenetic tracings of proteome size revealed a slowdown in innovation of the structural domain vocabulary and four regimes of allometric scaling that reflected a Heaps law. These regimes explained increasing economies of scale in the evolutionary growth and accretion of kernel proteome repertoires of viruses and cellular organisms that resemble growth of human languages with limited vocabulary sizes. Results reconcile dynamic and static views of domain frequency distributions that are consistent with the axiom of spatiotemporal continuity that is tenet of evolutionary thinking. PMID:28690608

Dimensions of Adolescent Subjective Social Status within the School Community: Description and Correlates

ERIC Educational Resources Information Center

Sweeting, Helen; West, Patrick; Young, Robert; Kelly, Shona

2011-01-01

School pupils strive to meet both school-defined and social goals, and the structure of adolescent self-concept is multidimensional, including both academic and non-academic self-perceptions. However, subjective social status within the school community has been represented as a single dimension. Scottish 15-year olds participating in a…

Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM.

PubMed

Tuncbag, Nurcan; Gursoy, Attila; Nussinov, Ruth; Keskin, Ozlem

2011-08-11

Prediction of protein-protein interactions at the structural level on the proteome scale is important because it allows prediction of protein function, helps drug discovery and takes steps toward genome-wide structural systems biology. We provide a protocol (termed PRISM, protein interactions by structural matching) for large-scale prediction of protein-protein interactions and assembly of protein complex structures. The method consists of two components: rigid-body structural comparisons of target proteins to known template protein-protein interfaces and flexible refinement using a docking energy function. The PRISM rationale follows our observation that globally different protein structures can interact via similar architectural motifs. PRISM predicts binding residues by using structural similarity and evolutionary conservation of putative binding residue 'hot spots'. Ultimately, PRISM could help to construct cellular pathways and functional, proteome-scale annotation. PRISM is implemented in Python and runs in a UNIX environment. The program accepts Protein Data Bank-formatted protein structures and is available at http://prism.ccbb.ku.edu.tr/prism_protocol/.

Proteomic landscape in Central and Eastern Europe: the 9th Central and Eastern European Proteomic Conference, Poznań, Poland.

PubMed

Gadher, Suresh Jivan; Marczak, Łukasz; Łuczak, Magdalena; Stobiecki, Maciej; Widlak, Piotr; Kovarova, Hana

2016-01-01

Every year since 2007, the Central and Eastern European Proteomic Conference (CEEPC) has excelled in representing state-of-the-art proteomics in and around Central and Eastern Europe, and linking it to international institutions worldwide. Its mission remains to contribute to all approaches of proteomics including traditional and often-revisited methodologies as well as the latest technological achievements in clinical, quantitative and structural proteomics with a view to systems biology of a variety of processes. The 9th CEEPC was held from June 15th to 18th, 2015, at the Institute of Bioorganic Chemistry, Polish Academy of Sciences in Poznań, Poland. The scientific program stimulated exchange of proteomic knowledge whilst the spectacular venue of the conference allowed participants to enjoy the cobblestoned historical city of Poznań.

The path to enlightenment: making sense of genomic and proteomic information.

PubMed

Maurer, Martin H

2004-05-01

Whereas genomics describes the study of genome, mainly represented by its gene expression on the DNA or RNA level, the term proteomics denotes the study of the proteome, which is the protein complement encoded by the genome. In recent years, the number of proteomic experiments increased tremendously. While all fields of proteomics have made major technological advances, the biggest step was seen in bioinformatics. Biological information management relies on sequence and structure databases and powerful software tools to translate experimental results into meaningful biological hypotheses and answers. In this resource article, I provide a collection of databases and software available on the Internet that are useful to interpret genomic and proteomic data. The article is a toolbox for researchers who have genomic or proteomic datasets and need to put their findings into a biological context.

An Investigation into Customer Service Policies and Practices within the Scottish College Library Sector: A Comparison between the Customer Service Exemplars from the Retail Sector with Current Scottish College Library Practice

ERIC Educational Resources Information Center

Paterson, Neil

2011-01-01

The aim of this research project was to investigate the customer care methods within the Scottish college library sector. The researcher sought to compare examples of the customer care and service policies and practices from the sector with exemplars of good customer service from the retail sector. A qualitative, grounded theory approach was…

Linking the proteins--elucidation of proteome-scale networks using mass spectrometry.

PubMed

Pflieger, Delphine; Gonnet, Florence; de la Fuente van Bentem, Sergio; Hirt, Heribert; de la Fuente, Alberto

2011-01-01

Proteomes are intricate. Typically, thousands of proteins interact through physical association and post-translational modifications (PTMs) to give rise to the emergent functions of cells. Understanding these functions requires one to study proteomes as "systems" rather than collections of individual protein molecules. The abstraction of the interacting proteome to "protein networks" has recently gained much attention, as networks are effective representations, that lose specific molecular details, but provide the ability to see the proteome as a whole. Mostly two aspects of the proteome have been represented by network models: proteome-wide physical protein-protein-binding interactions organized into Protein Interaction Networks (PINs), and proteome-wide PTM relations organized into Protein Signaling Networks (PSNs). Mass spectrometry (MS) techniques have been shown to be essential to reveal both of these aspects on a proteome-wide scale. Techniques such as affinity purification followed by MS have been used to elucidate protein-protein interactions, and MS-based quantitative phosphoproteomics is critical to understand the structure and dynamics of signaling through the proteome. We here review the current state-of-the-art MS-based analytical pipelines for the purpose to characterize proteome-scale networks. Copyright © 2010 Wiley Periodicals, Inc.

[Methods of quantitative proteomics].

PubMed

Kopylov, A T; Zgoda, V G

2007-01-01

In modern science proteomic analysis is inseparable from other fields of systemic biology. Possessing huge resources quantitative proteomics operates colossal information on molecular mechanisms of life. Advances in proteomics help researchers to solve complex problems of cell signaling, posttranslational modification, structure and functional homology of proteins, molecular diagnostics etc. More than 40 various methods have been developed in proteomics for quantitative analysis of proteins. Although each method is unique and has certain advantages and disadvantages all these use various isotope labels (tags). In this review we will consider the most popular and effective methods employing both chemical modifications of proteins and also metabolic and enzymatic methods of isotope labeling.

Proteome complexity and the forces that drive proteome imbalance

PubMed Central

Harper, J. Wade; Bennett, Eric J.

2016-01-01

Summary The cellular proteome is a complex microcosm of structural and regulatory networks that requires continuous surveillance and modification to meet the dynamic needs of the cell. It is therefore crucial that the protein flux of the cell remains in balance to ensure proper cell function. Genetic alterations that range from chromosome imbalance to oncogene activation can affect the speed, fidelity and capacity of protein biogenesis and degradation systems, which often results in proteome imbalance. An improved understanding of the causes and consequences of proteome imbalance is helping to reveal how these systems can be targeted to treat diseases such as cancer. PMID:27629639

The Triple Qualification examination of the Scottish medical and surgical colleges, 1884-1993.

PubMed

Dingwall, H M

2010-09-01

The Triple Qualification (TQ) examination of the three Scottish medical colleges was founded in 1884 in the aftermath of the Medical Act of 1858, to offer a medical qualification that would have equal status with that of the universities and other medical schools. Continued efforts to amend the Act had threatened that the universities might dominate basic medical education to the exclusion of the colleges, which opposed this perceived threat to their viability. The TQ proved surprisingly durable and catered for a changing constituency of candidates over the century of its existence, offering a route to medical qualification for individuals from Great Britain and Ireland, the dominions and such diverse groups as exiled Jews from Europe and Rhodesians following independence. This article examines the origins and structure of the examination and assesses the changing candidate profile over the century of its existence.

Expecting motherhood? Stratifying reproduction in twenty-first century Scottish abortion practice

PubMed Central

Beynon-Jones, Siân M.

2015-01-01

This article illustrates how Scottish health professionals involved in contemporary abortion provision construct stratified expectations about women’s reproductive decision-making. Drawing on 42 semi-structured interviews I reveal the contingent discourses through which health professionals constitute the ‘rationality’ of the female subject who requests abortion. Specifically, I illustrate how youth, age, parity and class are mobilised as criteria through which to distinguish ‘types’ of patient whose requests for abortion are deemed particularly understandable or particularly problematic. I conceptualise this process of differentiation as a form of ‘stratified reproduction’ (Colen, 1995; Ginsburg and Rapp, 1995) and argue that it is significant for two reasons. Firstly, it illustrates the operation of dominant discourses concerning abortion and motherhood in twenty-first century Britain. Secondly, it extends the forms of critique which feminist scholarship has, to date, developed of the regulation of abortion provision in the UK. PMID:25774067

Computer applications making rapid advances in high throughput microbial proteomics (HTMP).

PubMed

Anandkumar, Balakrishna; Haga, Steve W; Wu, Hui-Fen

2014-02-01

The last few decades have seen the rise of widely-available proteomics tools. From new data acquisition devices, such as MALDI-MS and 2DE to new database searching softwares, these new products have paved the way for high throughput microbial proteomics (HTMP). These tools are enabling researchers to gain new insights into microbial metabolism, and are opening up new areas of study, such as protein-protein interactions (interactomics) discovery. Computer software is a key part of these emerging fields. This current review considers: 1) software tools for identifying the proteome, such as MASCOT or PDQuest, 2) online databases of proteomes, such as SWISS-PROT, Proteome Web, or the Proteomics Facility of the Pathogen Functional Genomics Resource Center, and 3) software tools for applying proteomic data, such as PSI-BLAST or VESPA. These tools allow for research in network biology, protein identification, functional annotation, target identification/validation, protein expression, protein structural analysis, metabolic pathway engineering and drug discovery.

The Role of Higher Education within Broader Skills Policies, a Comparison of Emerging Scottish and English Approaches

ERIC Educational Resources Information Center

Keep, Ewart

2014-01-01

This article explores the important role played by higher education in broader skills and economic development policies in England and Scotland. It places the often divergent policy experiments and structural developments in these two countries' higher education systems within an international policy context and explains why England and Scotland…

Living in a Sweetie Culture: Scottish Parents' Difficulties in Maintaining Their Children's Oral Health

ERIC Educational Resources Information Center

Smith, Patricia Anne; Freeman, Ruth

2009-01-01

Objective: To investigate the views and experiences of parents whose children have rampant tooth decay. Methods: In-depth, semi-structured interviews were carried out with 19 parents of varied age and social background whose children had been referred to Dundee Dental Hospital for assessment for dental extractions. Participants were encouraged to…

Access Issues in Adult Vocational Guidance and Counselling for People at Risk of Social Exclusion. Perspectives from Two Qualitative Research Projects.

ERIC Educational Resources Information Center

Clayton, Pamela; McGill, Paul

2000-01-01

Two studies (of 105 Scottish adults returning to study and of social exclusion and lifelong learning) identified structural barriers in adult access to guidance services: rural location, disability, single parenthood, eldercare, homelessness, criminal record, and refugee status. Solutions include publicity, partnerships, outreach, and supportive…

Insular Celtic population structure and genomic footprints of migration

PubMed Central

Hellenthal, Garrett

2018-01-01

Previous studies of the genetic landscape of Ireland have suggested homogeneity, with population substructure undetectable using single-marker methods. Here we have harnessed the haplotype-based method fineSTRUCTURE in an Irish genome-wide SNP dataset, identifying 23 discrete genetic clusters which segregate with geographical provenance. Cluster diversity is pronounced in the west of Ireland but reduced in the east where older structure has been eroded by historical migrations. Accordingly, when populations from the neighbouring island of Britain are included, a west-east cline of Celtic-British ancestry is revealed along with a particularly striking correlation between haplotypes and geography across both islands. A strong relationship is revealed between subsets of Northern Irish and Scottish populations, where discordant genetic and geographic affinities reflect major migrations in recent centuries. Additionally, Irish genetic proximity of all Scottish samples likely reflects older strata of communication across the narrowest inter-island crossing. Using GLOBETROTTER we detected Irish admixture signals from Britain and Europe and estimated dates for events consistent with the historical migrations of the Norse-Vikings, the Anglo-Normans and the British Plantations. The influence of the former is greater than previously estimated from Y chromosome haplotypes. In all, we paint a new picture of the genetic landscape of Ireland, revealing structure which should be considered in the design of studies examining rare genetic variation and its association with traits. PMID:29370172

Genetics of Hereditary Ataxia in Scottish Terriers.

PubMed

Urkasemsin, G; Nielsen, D M; Singleton, A; Arepalli, S; Hernandez, D; Agler, C; Olby, N J

2017-07-01

Scottish Terriers have a high incidence of juvenile onset hereditary ataxia primarily affecting the Purkinje neuron of the cerebellar cortex and causing slowly progressive cerebellar dysfunction. To identify chromosomal regions associated with hereditary ataxia in Scottish Terriers. One hundred and fifty-three Scottish Terriers were recruited through the Scottish Terrier Club of America. Prospective study. Dogs were classified as affected if they had slowly progressive cerebellar signs. When possible, magnetic resonance imaging and histopathological evaluation of the brain were completed as diagnostic aids. To identify genomic regions connected with the disease, genome-wide mapping was performed using both linkage- and association-based approaches. Pedigree evaluation and homozygosity mapping were also performed to examine mode of inheritance and to investigate the region of interest, respectively. Linkage and genome-wide association studies in a cohort of Scottish Terriers both identified a region on CFA X strongly associated with the disease trait. Homozygosity mapping revealed a 4 Mb region of interest. Pedigree evaluation failed to identify the possible mode of inheritance due to the lack of complete litter information. This finding suggests that further genetic investigation of the potential region of interest on CFA X should be considered in order to identify the causal mutation as well as develop a genetic test to eliminate the disease from this breed. Copyright © 2017 The Authors. Journal of Veterinary Internal Medicine published by Wiley Periodicals, Inc. on behalf of the American College of Veterinary Internal Medicine.

Flood Risk Management Policy in Scotland: Research Questions Past, Present and Future

NASA Astrophysics Data System (ADS)

Wilkinson, Mark; Hastings, Emily; MacDonald, Jannette

2016-04-01

Scotland's Centre of Expertise for Waters (CREW) delivers accessible research and expert opinion to support the Scottish Government and its delivery partners in the development and implementation of water policy. It was established in 2011 by the Scottish Government (Rural and Environmental Science and Analytical Services) in recognition of a gap in the provision of short term advice and research to policy (development and implementation). Key policy areas include the Water Framework Directive, Floods Directive, Drinking Water Directive, Habitats Directive and Scotland's Hydro Nation Strategy. CREW is unique in its demand-driven and free service for policy makers and practitioners, managing the engagement between scientists, policy makers and practitioners to work effectively across this interface. The users of CREW are the Scottish Government, Scottish Environment Protection Agency, Scottish Natural Heritage and Scottish Water. CREW has funded around 100 projects relating to water policy since its inception in 2011. Of these, a significant number relate to flood risk management policy. Based on a review of work to date, this poster will give an overview of these projects and a forward look at the challenges that remain. From learning from community led flood risk management to surface water flood forecasting for urban communities, links will be made between sustainable and traditional flood risk management while considering the perceptions of stakeholders to flood risk management. How can we deliver fully integrated flood risk management options? How policy makers, scientists and land managers can better work together will also be explored.

The UniProtKB guide to the human proteome

PubMed Central

Breuza, Lionel; Poux, Sylvain; Estreicher, Anne; Famiglietti, Maria Livia; Magrane, Michele; Tognolli, Michael; Bridge, Alan; Baratin, Delphine; Redaschi, Nicole

2016-01-01

Advances in high-throughput and advanced technologies allow researchers to routinely perform whole genome and proteome analysis. For this purpose, they need high-quality resources providing comprehensive gene and protein sets for their organisms of interest. Using the example of the human proteome, we will describe the content of a complete proteome in the UniProt Knowledgebase (UniProtKB). We will show how manual expert curation of UniProtKB/Swiss-Prot is complemented by expert-driven automatic annotation to build a comprehensive, high-quality and traceable resource. We will also illustrate how the complexity of the human proteome is captured and structured in UniProtKB. Database URL: www.uniprot.org PMID:26896845

Gill pathology in Scottish farmed Atlantic salmon, Salmo salar L., associated with the microsporidian Desmozoon lepeophtherii Freeman et Sommerville, 2009.

PubMed

Matthews, C G G; Richards, R H; Shinn, A P; Cox, D I

2013-10-01

Gill disorders have emerged in recent years as a significant problem in the production of marine-stage Atlantic salmon Salmo salar L. The multi-aetiological condition 'proliferative gill inflammation' (PGI) has been reported to cause heavy losses in western Norway, yet reports of Scottish cases of the disease have remained anecdotal. In the present study, histopathological material from a marine production site in the Scottish Highlands experiencing mortalities due to a seasonal gill disease with proliferative-type pathology was examined using light microscopy, special staining techniques and transmission electron microscopy (TEM). The microsporidian Desmozoon lepeophtherii Freeman et Sommerville, 2009 (syn. Paranucleospora theridion) was identified by staining using a Gram Twort method and TEM associated with distinctive proliferative and necrotic pathology confined to the interlamellar Malpighian cell areas of the primary filaments. Epitheliocystis was not a feature of the gill pathology observed. It is believed this is the first report of D. lepeophtherii being identified associated with pathology in a Scottish gill disease case, and supports anecdotal reports that a disease at least partly synonymous with PGI as described by Norwegian researchers is present in Scottish aquaculture. © 2013 John Wiley & Sons Ltd.

Redox Proteomics: A Key Tool for New Insights into Protein Modification with Relevance to Disease.

PubMed

Butterfield, D Allan; Perluigi, Marzia

2017-03-01

Oxidatively modified proteins are characterized by elevations in protein-resident carbonyls or 3-nitrotyrosine, measures of protein oxidation, or protein bound reactive alkenals such as 4-hydroxy-2-nonenal, a measure of lipid peroxidation. Oxidatively modified proteins nearly always have altered structure and function. Redox proteomics is that branch of proteomics used to identify oxidized proteins and determine the extent and location of oxidative modifications in the proteomes of interest. This technique nearly always employs mass spectrometry as the major platform to achieve the goals of identifying the target proteins. Once identified, oxidatively modified proteins can be placed in specific molecular pathways to provide insights into protein oxidation and human disease. Both original research and review articles are included in this Forum on Redox Proteomics. The topics related to redox proteomics range from basic chemistry of sulfur radical-induced redox modifications in proteins, to the thiol secretome and inflammatory network, to reversible thiol oxidation in proteomes, to the role of glutamine synthetase in peripheral and central environments on inflammation and insulin resistance, to bioanalytical aspects of tyrosine nitrated proteins, to protein oxidation in human smokers and models thereof, and to Alzheimer disease, including articles on the brain ubiquitinylome and the "triangle of death" composed of oxidatively modified proteins involved in energy metabolism, mammalian target of rampamycin activation, and the proteostasis network. This Forum on Redox Proteomics is both timely and a critically important resource to highlight one of the key tools needed to better understand protein structure and function in oxidative environments in health and disease. Antioxid. Redox Signal. 26, 277-279.

The impact of proteomics on the understanding of functions and biogenesis of fungal extracellular vesicles.

PubMed

Rodrigues, Marcio L; Nakayasu, Ernesto S; Almeida, Igor C; Nimrichter, Leonardo

2014-01-31

Several microbial molecules are released to the extracellular space in vesicle-like structures. In pathogenic fungi, these molecules include pigments, polysaccharides, lipids, and proteins, which traverse the cell wall in vesicles that accumulate in the extracellular space. The diverse composition of fungal extracellular vesicles (EV) is indicative of multiple mechanisms of cellular biogenesis, a hypothesis that was supported by EV proteomic studies in a set of Saccharomyces cerevisiae strains with defects in both conventional and unconventional secretory pathways. In the human pathogens Cryptococcus neoformans, Histoplasma capsulatum, and Paracoccidioides brasiliensis, extracellular vesicle proteomics revealed the presence of proteins with both immunological and pathogenic activities. In fact, fungal EV have been demonstrated to interfere with the activity of immune effector cells and to increase fungal pathogenesis. In this review, we discuss the impact of proteomics on the understanding of functions and biogenesis of fungal EV, as well as the potential role of these structures in fungal pathogenesis. This article is part of a Special Issue entitled: Trends in Microbial Proteomics. Copyright © 2013 Elsevier B.V. All rights reserved.

Time, space, and disorder in the expanding proteome universe.

PubMed

Minde, David-Paul; Dunker, A Keith; Lilley, Kathryn S

2017-04-01

Proteins are highly dynamic entities. Their myriad functions require specific structures, but proteins' dynamic nature ranges all the way from the local mobility of their amino acid constituents to mobility within and well beyond single cells. A truly comprehensive view of the dynamic structural proteome includes: (i) alternative sequences, (ii) alternative conformations, (iii) alternative interactions with a range of biomolecules, (iv) cellular localizations, (v) alternative behaviors in different cell types. While these aspects have traditionally been explored one protein at a time, we highlight recently emerging global approaches that accelerate comprehensive insights into these facets of the dynamic nature of protein structure. Computational tools that integrate and expand on multiple orthogonal data types promise to enable the transition from a disjointed list of static snapshots to a structurally explicit understanding of the dynamics of cellular mechanisms. © 2017 The Authors. Proteomics Published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A comparative study of the course-related family and financial problems of mature nursing students in Scotland and Australia.

PubMed

Cuthbertson, Philip; Lauder, William; Steele, Rebekah; Cleary, Sonja; Bradshaw, Julie

2004-07-01

This study reports a comparative survey of mature students undertaking pre-registration undergraduate nursing education in Australia and Scotland. The study aimed to explore comparisons between the course-related and course-related financial difficulties faced by mature students in two very different educational and funding systems. Financial stress is a predictor of both physical and mental health problems. A similar pattern of course-related problems were reported by both Australian and Scottish students with the exception that Scottish students experienced more problems with childcare and caring for elderly relatives. Course-related problems may be inherent in the nature of undergraduate nursing education although the relatively time-intensive nature of Scottish curricula may explain the childcare and elderly relatives difference. Scottish students reported higher overall financial-related problems but Australian students reported more problems with funding placements. These findings have implications for both curriculum designers and policy makers.

Exploring the Contribution of Workplace Learning to an HRD Strategy in the Scottish Legal Profession

ERIC Educational Resources Information Center

Watson, Sandra; Harmel-Law, Amanda

2010-01-01

Purpose: The purpose of this paper is to explore the relevance of human resource development (HRD) for law firms in the UK. It examines how the characteristics of legal professional practice in the UK, including the partnership structure, long established methods of targeting solicitors and the law society, may act as barriers to the…

The HUPO proteomics standards initiative--overcoming the fragmentation of proteomics data.

PubMed

Hermjakob, Henning

2006-09-01

Proteomics is a key field of modern biomolecular research, with many small and large scale efforts producing a wealth of proteomics data. However, the vast majority of this data is never exploited to its full potential. Even in publicly funded projects, often the raw data generated in a specific context is analysed, conclusions are drawn and published, but little attention is paid to systematic documentation, archiving, and public access to the data supporting the scientific results. It is often difficult to validate the results stated in a particular publication, and even simple global questions like "In which cellular contexts has my protein of interest been observed?" can currently not be answered with realistic effort, due to a lack of standardised reporting and collection of proteomics data. The Proteomics Standards Initiative (PSI), a work group of the Human Proteome Organisation (HUPO), defines community standards for data representation in proteomics to facilitate systematic data capture, comparison, exchange and verification. In this article we provide an overview of PSI organisational structure, activities, and current results, as well as ways to get involved in the broad-based, open PSI process.

Factors affecting the views and attitudes of Scottish pharmacists to continuing professional development.

PubMed

Power, Ailsa; Grammatiki, Aikaterini; Bates, Ian; Mc Kellar, Susan; Johnson, B Julienne; Diack, H Lesley; Stewart, Derek; Hudson, Steve A

2011-12-01

To explore factors associated with Scottish pharmacists' views and attitudes to continuing professional development (CPD). A retrospective principal component analysis of 552 (22.8%) questionnaires returned from a sample of 2420 Scottish pharmacists randomly selected from the 4300 pharmacists registered with the Royal Pharmaceutical Society of Great Britain and with a Scottish address. Principal component analysis of questionnaire items (n = 19) revealed four factors associated with Scottish pharmacists' views and attitudes to CPD: having positive support in the workplace, having access to resources and meeting learning needs, having confidence in the CPD process and motivation to participate in the CPD process. Community pharmacists were identified as the subgroup of pharmacists that needed most support for CPD regarding all four factors, while pharmacists working in primary care felt that they had most support in the workplace in comparison to other sectors (P < 0.05) and better access to resources and meeting learning needs when compared to community (P < 0.001) and hospital (P = 0.008) colleagues. Pharmacists working in primary care also felt more motivated to participate in the CPD process than those in the community (P < 0.001), and hospital pharmacists reported having more confidence in the CPD process compared to community pharmacists (P < 0.05). Using principal component analysis has identified four factors associated with Scottish pharmacists' views and attitudes to CPD. This may provide an approach to facilitate comparison of CPD views and attitudes with intra and inter professional groupings. Further study may allow identification of good practice and solutions to common CPD issues. © 2011 The Authors. IJPP © 2011 Royal Pharmaceutical Society.

Detection of Zn2+ release in nitric oxide treated cells and proteome: dependence on fluorescent sensor and proteomic sulfhydryl groups.

PubMed

Karim, Mohammad R; Petering, David H

2017-04-19

Nitric oxide (NO) is both an important regulatory molecule in biological systems and a toxic xenobiotic. Its oxidation products react with sulfhydryl groups and either nitrosylate or oxidize them. The aerobic reaction of NO supplied by diethylamine NONOate (DEA-NO) with pig kidney LLC-PK 1 cells and Zn-proteins within the isolated proteome was examined with three fluorescent zinc sensors, zinquin (ZQ), TSQ, and FluoZin-3 (FZ-3). Observations of Zn 2+ labilization from Zn-proteins depended on the specific sensor used. Upon cellular exposure to DEA-NO, ZQ sequestered about 13% of the proteomic Zn 2+ as Zn(ZQ) 2 and additional Zn 2+ as proteome·Zn-ZQ ternary complexes. TSQ, a sensor structurally related to ZQ with lower affinity for Zn 2+ , did not form Zn(TSQ) 2 . Instead, Zn 2+ mobilized by DEA-NO was exclusively bound as proteome·Zn-TSQ adducts. Analogous reactions of proteome with ZQ or TSQ in vitro displayed qualitatively similar products. Titration of native proteome with Zn 2+ in the presence of ZQ resulted in the sole formation of proteome·Zn-ZQ species. This result suggested that sulfhydryl groups are involved in non-specific proteomic binding of mobile Zn 2+ and that the appearance of Zn(ZQ) 2 after exposure of cells and proteome to DEA-NO resulted from a reduction in proteomic sulfhydryl ligands, favoring the formation of Zn(ZQ) 2 instead of proteome·Zn-ZQ. With the third sensor, FluoZin-3, neither Zn-FZ-3 nor proteome·Zn-FZ-3 was detected during the reaction of proteome with DEA-NO. Instead, it reacted independently with DEA-NO with a modest enhancement of fluorescence.

Dentistry proteomics: from laboratory development to clinical practice.

PubMed

Rezende, Taia M B; Lima, Stella M F; Petriz, Bernardo A; Silva, Osmar N; Freire, Mirna S; Franco, Octávio L

2013-12-01

Despite all the dental information acquired over centuries and the importance of proteome research, the cross-link between these two areas only emerged around mid-nineties. Proteomic tools can help dentistry in the identification of risk factors, early diagnosis, prevention, and systematic control that will promote the evolution of treatment in all dentistry specialties. This review mainly focuses on the evolution of dentistry in different specialties based on proteomic research and how these tools can improve knowledge in dentistry. The subjects covered are an overview of proteomics in dentistry, specific information on different fields in dentistry (dental structure, restorative dentistry, endodontics, periodontics, oral pathology, oral surgery, and orthodontics) and future directions. There are many new proteomic technologies that have never been used in dentistry studies and some dentistry areas that have never been explored by proteomic tools. It is expected that a greater integration of these areas will help to understand what is still unknown in oral health and disease. Copyright © 2013 Wiley Periodicals, Inc.

Low Cost, Scalable Proteomics Data Analysis Using Amazon's Cloud Computing Services and Open Source Search Algorithms

PubMed Central

Halligan, Brian D.; Geiger, Joey F.; Vallejos, Andrew K.; Greene, Andrew S.; Twigger, Simon N.

2009-01-01

One of the major difficulties for many laboratories setting up proteomics programs has been obtaining and maintaining the computational infrastructure required for the analysis of the large flow of proteomics data. We describe a system that combines distributed cloud computing and open source software to allow laboratories to set up scalable virtual proteomics analysis clusters without the investment in computational hardware or software licensing fees. Additionally, the pricing structure of distributed computing providers, such as Amazon Web Services, allows laboratories or even individuals to have large-scale computational resources at their disposal at a very low cost per run. We provide detailed step by step instructions on how to implement the virtual proteomics analysis clusters as well as a list of current available preconfigured Amazon machine images containing the OMSSA and X!Tandem search algorithms and sequence databases on the Medical College of Wisconsin Proteomics Center website (http://proteomics.mcw.edu/vipdac). PMID:19358578

Low cost, scalable proteomics data analysis using Amazon's cloud computing services and open source search algorithms.

PubMed

Halligan, Brian D; Geiger, Joey F; Vallejos, Andrew K; Greene, Andrew S; Twigger, Simon N

2009-06-01

One of the major difficulties for many laboratories setting up proteomics programs has been obtaining and maintaining the computational infrastructure required for the analysis of the large flow of proteomics data. We describe a system that combines distributed cloud computing and open source software to allow laboratories to set up scalable virtual proteomics analysis clusters without the investment in computational hardware or software licensing fees. Additionally, the pricing structure of distributed computing providers, such as Amazon Web Services, allows laboratories or even individuals to have large-scale computational resources at their disposal at a very low cost per run. We provide detailed step-by-step instructions on how to implement the virtual proteomics analysis clusters as well as a list of current available preconfigured Amazon machine images containing the OMSSA and X!Tandem search algorithms and sequence databases on the Medical College of Wisconsin Proteomics Center Web site ( http://proteomics.mcw.edu/vipdac ).

"Attacking the Citadel": James Moncreiff's Proposals to Reform Scottish Education, 1851-69.

ERIC Educational Resources Information Center

Bain, Wilson H.

1978-01-01

A review of the parliamentary actions of Lord Advocate James Moncreiff to create a fully national Scottish educational system against the opposition by church groups reluctant to lose control over parish schools and schoolmasters. (SJL)

Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms

PubMed Central

Nasir, Arshan; Naeem, Aisha; Khan, Muhammad Jawad; Lopez-Nicora, Horacio D.; Caetano-Anollés, Gustavo

2011-01-01

The functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. The molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using hidden Markov models of structural recognition. Here we analyze the functional annotation of protein domain structures in almost a thousand sequenced genomes, exploring the functional and structural diversity of proteomes. We find there is a remarkable conservation in the distribution of domains with respect to the molecular functions they perform in the three superkingdoms of life. In general, most of the protein repertoire is spent in functions related to metabolic processes but there are significant differences in the usage of domains for regulatory and extra-cellular processes both within and between superkingdoms. Our results support the hypotheses that the proteomes of superkingdom Eukarya evolved via genome expansion mechanisms that were directed towards innovating new domain architectures for regulatory and extra/intracellular process functions needed for example to maintain the integrity of multicellular structure or to interact with environmental biotic and abiotic factors (e.g., cell signaling and adhesion, immune responses, and toxin production). Proteomes of microbial superkingdoms Archaea and Bacteria retained fewer numbers of domains and maintained simple and smaller protein repertoires. Viruses appear to play an important role in the evolution of superkingdoms. We finally identify few genomic outliers that deviate significantly from the conserved functional design. These include Nanoarchaeum equitans, proteobacterial symbionts of insects with extremely reduced genomes, Tenericutes and Guillardia theta. These organisms spend most of their domains on information functions, including translation and transcription, rather than on metabolism and harbor a domain repertoire characteristic of parasitic organisms. In contrast, the functional repertoire of the proteomes of the Planctomycetes-Verrucomicrobia-Chlamydiae superphylum was no different than the rest of bacteria, failing to support claims of them representing a separate superkingdom. In turn, Protista and Bacteria shared similar functional distribution patterns suggesting an ancestral evolutionary link between these groups. PMID:24710297

Micro-proteomics with iterative data analysis: Proteome analysis in C. elegans at the single worm level.

PubMed

Bensaddek, Dalila; Narayan, Vikram; Nicolas, Armel; Murillo, Alejandro Brenes; Gartner, Anton; Kenyon, Cynthia J; Lamond, Angus I

2016-02-01

Proteomics studies typically analyze proteins at a population level, using extracts prepared from tens of thousands to millions of cells. The resulting measurements correspond to average values across the cell population and can mask considerable variation in protein expression and function between individual cells or organisms. Here, we report the development of micro-proteomics for the analysis of Caenorhabditis elegans, a eukaryote composed of 959 somatic cells and ∼1500 germ cells, measuring the worm proteome at a single organism level to a depth of ∼3000 proteins. This includes detection of proteins across a wide dynamic range of expression levels (>6 orders of magnitude), including many chromatin-associated factors involved in chromosome structure and gene regulation. We apply the micro-proteomics workflow to measure the global proteome response to heat-shock in individual nematodes. This shows variation between individual animals in the magnitude of proteome response following heat-shock, including variable induction of heat-shock proteins. The micro-proteomics pipeline thus facilitates the investigation of stochastic variation in protein expression between individuals within an isogenic population of C. elegans. All data described in this study are available online via the Encyclopedia of Proteome Dynamics (http://www.peptracker.com/epd), an open access, searchable database resource. © 2015 The Authors. PROTEOMICS Published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Impact of socioeconomic deprivation on rate and cause of death in severe mental illness.

PubMed

Martin, Julie Langan; McLean, Gary; Park, John; Martin, Daniel J; Connolly, Moira; Mercer, Stewart W; Smith, Daniel J

2014-09-12

Socioeconomic status has important associations with disease-specific mortality in the general population. Although individuals with Severe Mental Illnesses (SMI) experience significant premature mortality, the relationship between socioeconomic status and mortality in this group remains under investigated. We aimed to assess the impact of socioeconomic status on rate and cause of death in individuals with SMI (schizophrenia and bipolar disorder) relative to the local (Glasgow) and wider (Scottish) populations. Cause and age of death during 2006-2010 inclusive for individuals with schizophrenia or bipolar disorder registered on the Glasgow Psychosis Clinical Information System (PsyCIS) were obtained by linkage to the Scottish General Register Office (GRO). Rate and cause of death by socioeconomic status, measured by Scottish Index of Multiple Deprivation (SIMD), were compared to the Glasgow and Scottish populations. Death rates were higher in people with SMI across all socioeconomic quintiles compared to the Glasgow and Scottish populations, and persisted when suicide was excluded. Differences were largest in the most deprived quintile (794.6 per 10,000 population vs. 274.7 and 252.4 for Glasgow and Scotland respectively). Cause of death varied by socioeconomic status. For those living in the most deprived quintile, higher drug-related deaths occurred in those with SMI compared to local Glasgow and wider Scottish population rates (12.3% vs. 5.9%, p = <0.001 and 5.1% p = 0.002 respectively). A lower proportion of deaths due to cancer in those with SMI living in the most deprived quintile were also observed, relative to the local Glasgow and wider Scottish populations (12.3% vs. 25.1% p = 0.013 and 26.3% p = <0.001). The proportion of suicides was significantly higher in those with SMI living in the more affluent quintiles relative to Glasgow and Scotland (54.6% vs. 5.8%, p = <0.001 and 5.5%, p = <0.001). Excess mortality in those with SMI occurred across all socioeconomic quintiles compared to the Glasgow and Scottish populations but was most marked in the most deprived quintiles when suicide was excluded as a cause of death. Further work assessing the impact of socioeconomic status on specific causes of premature mortality in SMI is needed.

Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation

PubMed Central

Chen, Ke; Gao, Ye; Mih, Nathan; O’Brien, Edward J.; Yang, Laurence; Palsson, Bernhard O.

2017-01-01

Maintenance of a properly folded proteome is critical for bacterial survival at notably different growth temperatures. Understanding the molecular basis of thermoadaptation has progressed in two main directions, the sequence and structural basis of protein thermostability and the mechanistic principles of protein quality control assisted by chaperones. Yet we do not fully understand how structural integrity of the entire proteome is maintained under stress and how it affects cellular fitness. To address this challenge, we reconstruct a genome-scale protein-folding network for Escherichia coli and formulate a computational model, FoldME, that provides statistical descriptions of multiscale cellular response consistent with many datasets. FoldME simulations show (i) that the chaperones act as a system when they respond to unfolding stress rather than achieving efficient folding of any single component of the proteome, (ii) how the proteome is globally balanced between chaperones for folding and the complex machinery synthesizing the proteins in response to perturbation, (iii) how this balancing determines growth rate dependence on temperature and is achieved through nonspecific regulation, and (iv) how thermal instability of the individual protein affects the overall functional state of the proteome. Overall, these results expand our view of cellular regulation, from targeted specific control mechanisms to global regulation through a web of nonspecific competing interactions that modulate the optimal reallocation of cellular resources. The methodology developed in this study enables genome-scale integration of environment-dependent protein properties and a proteome-wide study of cellular stress responses. PMID:29073085

Less is More: Membrane Protein Digestion Beyond Urea–Trypsin Solution for Next-level Proteomics*

PubMed Central

Zhang, Xi

2015-01-01

The goal of next-level bottom-up membrane proteomics is protein function investigation, via high-coverage high-throughput peptide-centric quantitation of expression, modifications and dynamic structures at systems scale. Yet efficient digestion of mammalian membrane proteins presents a daunting barrier, and prevalent day-long urea–trypsin in-solution digestion proved insufficient to reach this goal. Many efforts contributed incremental advances over past years, but involved protein denaturation that disconnected measurement from functional states. Beyond denaturation, the recent discovery of structure/proteomics omni-compatible detergent n-dodecyl-β-d-maltopyranoside, combined with pepsin and PNGase F columns, enabled breakthroughs in membrane protein digestion: a 2010 DDM-low-TCEP (DLT) method for H/D-exchange (HDX) using human G protein-coupled receptor, and a 2015 flow/detergent-facilitated protease and de-PTM digestions (FDD) for integrative deep sequencing and quantitation using full-length human ion channel complex. Distinguishing protein solubilization from denaturation, protease digestion reliability from theoretical specificity, and reduction from alkylation, these methods shifted day(s)-long paradigms into minutes, and afforded fully automatable (HDX)-protein-peptide-(tandem mass tag)-HPLC pipelines to instantly measure functional proteins at deep coverage, high peptide reproducibility, low artifacts and minimal leakage. Promoting—not destroying—structures and activities harnessed membrane proteins for the next-level streamlined functional proteomics. This review analyzes recent advances in membrane protein digestion methods and highlights critical discoveries for future proteomics. PMID:26081834

Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya

PubMed Central

2012-01-01

Background The discovery of giant viruses with genome and physical size comparable to cellular organisms, remnants of protein translation machinery and virus-specific parasites (virophages) have raised intriguing questions about their origin. Evidence advocates for their inclusion into global phylogenomic studies and their consideration as a distinct and ancient form of life. Results Here we reconstruct phylogenies describing the evolution of proteomes and protein domain structures of cellular organisms and double-stranded DNA viruses with medium-to-very-large proteomes (giant viruses). Trees of proteomes define viruses as a ‘fourth supergroup’ along with superkingdoms Archaea, Bacteria, and Eukarya. Trees of domains indicate they have evolved via massive and primordial reductive evolutionary processes. The distribution of domain structures suggests giant viruses harbor a significant number of protein domains including those with no cellular representation. The genomic and structural diversity embedded in the viral proteomes is comparable to the cellular proteomes of organisms with parasitic lifestyles. Since viral domains are widespread among cellular species, we propose that viruses mediate gene transfer between cells and crucially enhance biodiversity. Conclusions Results call for a change in the way viruses are perceived. They likely represent a distinct form of life that either predated or coexisted with the last universal common ancestor (LUCA) and constitute a very crucial part of our planet’s biosphere. PMID:22920653

Dissecting plasmodesmata molecular composition by mass spectrometry-based proteomics.

PubMed

Salmon, Magali S; Bayer, Emmanuelle M F

2012-01-01

In plants, the intercellular communication through the membranous channels called plasmodesmata (PD; singular plasmodesma) plays pivotal roles in the orchestration of development, defence responses, and viral propagation. PD are dynamic structures embedded in the plant cell wall that are defined by specialized domains of the endoplasmic reticulum (ER) and the plasma membrane (PM). PD structure and unique functions are guaranteed by their particular molecular composition. Yet, up to recent years and despite numerous approaches such as mutant screens, immunolocalization, or screening of random cDNAs, only few PD proteins had been conclusively identified and characterized. A clear breakthrough in the search of PD constituents came from mass-spectrometry-based proteomic approaches coupled with subcellular fractionation strategies. Due to their position, firmly anchored in the extracellular matrix, PD are notoriously difficult to isolate for biochemical analysis. Proteomic-based approaches have therefore first relied on the use of cell wall fractions containing embedded PD then on "free" PD fractions whereby PD membranes were released from the walls by enzymatic degradation. To discriminate between likely contaminants and PD protein candidates, bioinformatics tools have often been used in combination with proteomic approaches. GFP fusion proteins of selected candidates have confirmed the PD association of several protein families. Here we review the accomplishments and limitations of the proteomic-based strategies to unravel the functional and structural complexity of PD. We also discuss the role of the identified PD-associated proteins.

Scottish Stroke Research Network: the first three years.

PubMed

McCormick, K; Langhorne, P; Graham, F E J; McFarlane, C

2010-08-01

Research networks were introduced in the UK to facilitate and improve clinical research and stroke was seen as a priority topic for local research network development. The Scottish Stroke Research Network (SSRN) is one of 11 stroke research networks in the UK. In this article we review the progress of the Scottish Stroke Research Network in the three years since inception. Between 2006-2009 the number of active hospital research sites has increased from 10 to 22 expanding to involve 20 stroke research nurses. There was a corresponding 58% increase in recruitment of participants into stroke studies, from 376 in 2006/07 to 594 in 2008/09. The majority (17/20) of our current studies are interventional. Data from one of these, the CLOTs trial (Clots in Legs Or sTocking after Stroke), demonstrates that the annual recruitment in Scotland increased from a median of 94 (range 6-122) patients per year in the six years before the SSRN, to 140 (135-158) patients per year after SSRN involvement. We currently screen about 50% of Scottish stroke patients and approximately 5% of Scottish stroke patients are participating in research studies that we support. The SSRN has made good progress in the first three years. Increasing the recruitment of screened patients remains a challenge.

Short-run economic effects of the Scottish smoking ban.

PubMed

Adda, Jérôme; Berlinski, Samuel; Machin, Stephen

2007-02-01

We estimated the short-run economic impacts of the Scottish smoking ban on public houses. Previous findings on the effect of smoking bans on the hospitality sector have mainly focused on the United States. These studies have mostly found no negative economic effects of such legislation on the hospitality sector in the long run. However, differences in the social use of public houses in Great Britain in comparison with the United States may lead to different findings. We used a quasi-experimental research design that compared the sales and number of customers in public houses located in Scotland before and after the Scottish smoking ban was introduced, relative to a control group of establishments across the English border where no ban was imposed. To perform this analysis, we collected data on 2724 pubs, 1590 in Scotland and 1134 in Northern England by phone interviews using quota sampling. We found that the Scottish ban led to a 10% decrease in sales [P = 0.02, 95% confidence interval (CI) -19% to -2%] and a 14% decrease in customers (P = 0.02, 95% CI -26% to -2%). Our study suggests that the Scottish smoking ban had a negative economic impact on public houses, at least in the short run, due in part to a drop in the number of customers.

Birth of plant proteomics in India: a new horizon.

PubMed

Narula, Kanika; Pandey, Aarti; Gayali, Saurabh; Chakraborty, Niranjan; Chakraborty, Subhra

2015-09-08

In the post-genomic era, proteomics is acknowledged as the next frontier for biological research. Although India has a long and distinguished tradition in protein research, the initiation of proteomics studies was a new horizon. Protein research witnessed enormous progress in protein separation, high-resolution refinements, biochemical identification of the proteins, protein-protein interaction, and structure-function analysis. Plant proteomics research, in India, began its journey on investigation of the proteome profiling, complexity analysis, protein trafficking, and biochemical modeling. The research article by Bhushan et al. in 2006 marked the birth of the plant proteomics research in India. Since then plant proteomics studies expanded progressively and are now being carried out in various institutions spread across the country. The compilation presented here seeks to trace the history of development in the area during the past decade based on publications till date. In this review, we emphasize on outcomes of the field providing prospects on proteomic pathway analyses. Finally, we discuss the connotation of strategies and the potential that would provide the framework of plant proteome research. The past decades have seen rapidly growing number of sequenced plant genomes and associated genomic resources. To keep pace with this increasing body of data, India is in the provisional phase of proteomics research to develop a comparative hub for plant proteomes and protein families, but it requires a strong impetus from intellectuals, entrepreneurs, and government agencies. Here, we aim to provide an overview of past, present and future of Indian plant proteomics, which would serve as an evaluation platform for those seeking to incorporate proteomics into their research programs. This article is part of a Special Issue entitled: Proteomics in India. Copyright © 2015 Elsevier B.V. All rights reserved.

Employee Spotlight: Clarence Chang | Argonne National Laboratory

Science.gov Websites

batteries --Electricity transmission --Smart Grid Environment -Biology --Computational biology --Environmental biology ---Metagenomics ---Terrestrial ecology --Molecular biology ---Clinical proteomics and biomarker discovery ---Interventional biology ---Proteomics --Structural biology -Environmental science &

A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhagavat, Raghu; Kim, Heung -Bok; Kim, Chang -Yub

Nucleoside tri-phosphates (NTP) form an important class of small molecule ligands that participate in, and are essential to a large number of biological processes. Here, we seek to identify the NTP binding proteome (NTPome) in M. tuberculosis (M.tb), a deadly pathogen. Identifying the NTPome is useful not only for gaining functional insights of the individual proteins but also for identifying useful drug targets. From an earlier study, we had structural models of M.tb at a proteome scale from which a set of 13,858 small molecule binding pockets were identified. We use a set of NTP binding sub-structural motifs derived frommore » a previous study and scan the M.tb pocketome, and find that 1,768 proteins or 43% of the proteome can theoretically bind NTP ligands. Using an experimental proteomics approach involving dye-ligand affinity chromatography, we confirm NTP binding to 47 different proteins, of which 4 are hypothetical proteins. Our analysis also provides the precise list of binding site residues in each case, and the probable ligand binding pose. In conclusion, as the list includes a number of known and potential drug targets, the identification of NTP binding can directly facilitate structure-based drug design of these targets.« less

A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis

DOE PAGES

Bhagavat, Raghu; Kim, Heung -Bok; Kim, Chang -Yub; ...

2017-10-02

Nucleoside tri-phosphates (NTP) form an important class of small molecule ligands that participate in, and are essential to a large number of biological processes. Here, we seek to identify the NTP binding proteome (NTPome) in M. tuberculosis (M.tb), a deadly pathogen. Identifying the NTPome is useful not only for gaining functional insights of the individual proteins but also for identifying useful drug targets. From an earlier study, we had structural models of M.tb at a proteome scale from which a set of 13,858 small molecule binding pockets were identified. We use a set of NTP binding sub-structural motifs derived frommore » a previous study and scan the M.tb pocketome, and find that 1,768 proteins or 43% of the proteome can theoretically bind NTP ligands. Using an experimental proteomics approach involving dye-ligand affinity chromatography, we confirm NTP binding to 47 different proteins, of which 4 are hypothetical proteins. Our analysis also provides the precise list of binding site residues in each case, and the probable ligand binding pose. In conclusion, as the list includes a number of known and potential drug targets, the identification of NTP binding can directly facilitate structure-based drug design of these targets.« less

Duration of daily TV/screen watching with cardiovascular, respiratory, mental and psychiatric health: Scottish Health Survey, 2012-2013.

PubMed

Shiue, Ivy

2015-01-01

The link of duration of TV and/or screen watching and chronic health conditions by subtypes is unclear. Therefore, the relationship between TV and/or screen watching hours and cardiovascular, respiratory, mental and psychiatric health and well-being (happiness) was assessed in an independent population-based survey to identify correlations of various hours with health conditions. Data was retrieved from the Scottish Health Survey, 2012-2013. Information on demographics, lifestyle factors, self-reported health conditions and TV and/or screen watching duration in both Scottish adults and children was collected by annual household interviews. Chi-square test and survey weighted logistic and multi-nominal modelling were performed. 5527 (57.0%) Scottish adults aged 16-99 watched TV and/or screen daily for 3 + h on average. There was a trend toward more hypertension, angina, stroke, diabetes, chronic obstructive pulmonary disease and poor self-rated health and mental health. Reporting watching TV and/or screen for 4 + h, for 5 + h and for 8 + h was associated with higher rates of heart attack, heart murmur or other heart troubles and abnormal heart rhythms, respectively. 414 (20.7%) Scottish children aged 4-12 watched TV and/or screen for 3h or more. They tended to have poor self-rated health and life difficulties perceived as emotional and behavioural problems. There were associations between various hours of TV and/or screen watching (3+h) and poor health observed both in Scottish adults and children. Future educational and public health programmes minimising TV and/or screen watching in order to protect cardiovascular, respiratory, mental and psychiatric health might be considered. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Scottish Antimicrobial Prescribing Group (SAPG): development and impact of the Scottish National Antimicrobial Stewardship Programme.

PubMed

Nathwani, Dilip; Sneddon, Jacqueline; Malcolm, William; Wiuff, Camilla; Patton, Andrea; Hurding, Simon; Eastaway, Anne; Seaton, R Andrew; Watson, Emma; Gillies, Elizabeth; Davey, Peter; Bennie, Marion

2011-07-01

In 2008, the Scottish Management of Antimicrobial Resistance Action Plan (ScotMARAP) was published by the Scottish Government. One of the key actions was initiation of the Scottish Antimicrobial Prescribing Group (SAPG), hosted within the Scottish Medicines Consortium, to take forward national implementation of the key recommendations of this action plan. The primary objective of SAPG is to co-ordinate and deliver a national framework or programme of work for antimicrobial stewardship. This programme, led by SAPG, is delivered by NHS National Services Scotland (Health Protection Scotland and Information Services Division), NHS Quality Improvement Scotland, and NHS National Education Scotland as well as NHS board Antimicrobial Management Teams. Between 2008 and 2010, SAPG has achieved a number of early successes, which are the subject of this review: (i) through measures to optimise prescribing in hospital and primary care, combined with infection prevention measures, SAPG has contributed significantly to reducing Clostridium difficile infection rates in Scotland; (ii) there has been engagement of all key stakeholders at local and national levels to ensure an integrated approach to antimicrobial stewardship within the wider healthcare-associated infection agenda; (iii) development and implementation of data management systems to support quality improvement; (iv) development of training materials on antimicrobial stewardship for healthcare professionals; and (v) improving clinical management of infections (e.g. community-acquired pneumonia) through quality improvement methodology. The early successes achieved by SAPG demonstrate that this delivery model is effective and provides the leadership and focus required to implement antimicrobial stewardship to improve antimicrobial prescribing and infection management across NHS Scotland. Copyright © 2011 Elsevier B.V. and the International Society of Chemotherapy. All rights reserved.

Inpatient costs for people with type 1 and type 2 diabetes in Scotland: a study from the Scottish Diabetes Research Network Epidemiology Group.

PubMed

Govan, L; Wu, O; Briggs, A; Colhoun, H M; McKnight, J A; Morris, A D; Pearson, D W M; Petrie, J R; Sattar, N; Wild, S H; Lindsay, R S

2011-08-01

The rising prevalence of diabetes worldwide has increased interest in the cost of diabetes. Inpatient costs for all people with diabetes in Scotland were investigated. The Scottish Care Information-Diabetes Collaboration (SCI-DC), a real-time clinical information system of almost all diagnosed cases of diabetes in Scotland, UK, was linked to data on all hospital admissions for people with diabetes. Inpatient stay costs were estimated using the 2007-2008 Scottish National Tariff. The probability of hospital admission and total annual cost of admissions were estimated in relation to age, sex, type of diabetes, history of vascular admission, HbA(1c), creatinine, body mass index and diabetes duration. In Scotland during 2005-2007, 24,750 people with type 1 and 195,433 people with type 2 diabetes were identified, accounting for approximately 4.3% of the total Scottish population (5.1 million). The estimated total annual cost of admissions for all people diagnosed with type 1 and type 2 diabetes was £26 million and £275 million, respectively, approximately 12% of the total Scottish inpatient expenditure (£2.4 billion). Sex, increasing age, serum creatinine, previous vascular history and HbA(1c) (the latter differentially in type 1 and type 2) were all associated with likelihood and total annual cost of admission. Diabetes inpatient expenditure accounted for 12% of the total Scottish inpatient expenditure, whilst people with diabetes account for 4.3% of the population. Of the modifiable risk factors, HbA(1c) was the most important driver of cost in type 1 diabetes.

Application of proteomics to ecology and population biology.

PubMed

Karr, T L

2008-02-01

Proteomics is a relatively new scientific discipline that merges protein biochemistry, genome biology and bioinformatics to determine the spatial and temporal expression of proteins in cells, tissues and whole organisms. There has been very little application of proteomics to the fields of behavioral genetics, evolution, ecology and population dynamics, and has only recently been effectively applied to the closely allied fields of molecular evolution and genetics. However, there exists considerable potential for proteomics to impact in areas related to functional ecology; this review will introduce the general concepts and methodologies that define the field of proteomics and compare and contrast the advantages and disadvantages with other methods. Examples of how proteomics can aid, complement and indeed extend the study of functional ecology will be discussed including the main tool of ecological studies, population genetics with an emphasis on metapopulation structure analysis. Because proteomic analyses provide a direct measure of gene expression, it obviates some of the limitations associated with other genomic approaches, such as microarray and EST analyses. Likewise, in conjunction with associated bioinformatics and molecular evolutionary tools, proteomics can provide the foundation of a systems-level integration approach that can enhance ecological studies. It can be envisioned that proteomics will provide important new information on issues specific to metapopulation biology and adaptive processes in nature. A specific example of the application of proteomics to sperm ageing is provided to illustrate the potential utility of the approach.

Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML database--Xindice.

PubMed

Li, Feng; Li, Maoyu; Xiao, Zhiqiang; Zhang, Pengfei; Li, Jianling; Chen, Zhuchu

2006-01-11

Many proteomics initiatives require integration of all information with uniformcriteria from collection of samples and data display to publication of experimental results. The integration and exchanging of these data of different formats and structure imposes a great challenge to us. The XML technology presents a promise in handling this task due to its simplicity and flexibility. Nasopharyngeal carcinoma (NPC) is one of the most common cancers in southern China and Southeast Asia, which has marked geographic and racial differences in incidence. Although there are some cancer proteome databases now, there is still no NPC proteome database. The raw NPC proteome experiment data were captured into one XML document with Human Proteome Markup Language (HUP-ML) editor and imported into native XML database Xindice. The 2D/MS repository of NPC proteome was constructed with Apache, PHP and Xindice to provide access to the database via Internet. On our website, two methods, keyword query and click query, were provided at the same time to access the entries of the NPC proteome database. Our 2D/MS repository can be used to share the raw NPC proteomics data that are generated from gel-based proteomics experiments. The database, as well as the PHP source codes for constructing users' own proteome repository, can be accessed at http://www.xyproteomics.org/.

Toward the Standardization of Mitochondrial Proteomics: The Italian Mitochondrial Human Proteome Project Initiative.

PubMed

Alberio, Tiziana; Pieroni, Luisa; Ronci, Maurizio; Banfi, Cristina; Bongarzone, Italia; Bottoni, Patrizia; Brioschi, Maura; Caterino, Marianna; Chinello, Clizia; Cormio, Antonella; Cozzolino, Flora; Cunsolo, Vincenzo; Fontana, Simona; Garavaglia, Barbara; Giusti, Laura; Greco, Viviana; Lucacchini, Antonio; Maffioli, Elisa; Magni, Fulvio; Monteleone, Francesca; Monti, Maria; Monti, Valentina; Musicco, Clara; Petrosillo, Giuseppe; Porcelli, Vito; Saletti, Rosaria; Scatena, Roberto; Soggiu, Alessio; Tedeschi, Gabriella; Zilocchi, Mara; Roncada, Paola; Urbani, Andrea; Fasano, Mauro

2017-12-01

The Mitochondrial Human Proteome Project aims at understanding the function of the mitochondrial proteome and its crosstalk with the proteome of other organelles. Being able to choose a suitable and validated enrichment protocol of functional mitochondria, based on the specific needs of the downstream proteomics analysis, would greatly help the researchers in the field. Mitochondrial fractions from ten model cell lines were prepared using three enrichment protocols and analyzed on seven different LC-MS/MS platforms. All data were processed using neXtProt as reference database. The data are available for the Human Proteome Project purposes through the ProteomeXchange Consortium with the identifier PXD007053. The processed data sets were analyzed using a suite of R routines to perform a statistical analysis and to retrieve subcellular and submitochondrial localizations. Although the overall number of identified total and mitochondrial proteins was not significantly dependent on the enrichment protocol, specific line to line differences were observed. Moreover, the protein lists were mapped to a network representing the functional mitochondrial proteome, encompassing mitochondrial proteins and their first interactors. More than 80% of the identified proteins resulted in nodes of this network but with a different ability in coisolating mitochondria-associated structures for each enrichment protocol/cell line pair.

Proteomic insights into floral biology.

PubMed

Li, Xiaobai; Jackson, Aaron; Xie, Ming; Wu, Dianxing; Tsai, Wen-Chieh; Zhang, Sheng

2016-08-01

The flower is the most important biological structure for ensuring angiosperms reproductive success. Not only does the flower contain critical reproductive organs, but the wide variation in morphology, color, and scent has evolved to entice specialized pollinators, and arguably mankind in many cases, to ensure the successful propagation of its species. Recent proteomic approaches have identified protein candidates related to these flower traits, which has shed light on a number of previously unknown mechanisms underlying these traits. This review article provides a comprehensive overview of the latest advances in proteomic research in floral biology according to the order of flower structure, from corolla to male and female reproductive organs. It summarizes mainstream proteomic methods for plant research and recent improvements on two dimensional gel electrophoresis and gel-free workflows for both peptide level and protein level analysis. The recent advances in sequencing technologies provide a new paradigm for the ever-increasing genome and transcriptome information on many organisms. It is now possible to integrate genomic and transcriptomic data with proteomic results for large-scale protein characterization, so that a global understanding of the complex molecular networks in flower biology can be readily achieved. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock. Copyright © 2016 Elsevier B.V. All rights reserved.

Detergents: Friends not foes for high-performance membrane proteomics toward precision medicine.

PubMed

Zhang, Xi

2017-02-01

Precision medicine, particularly therapeutics, emphasizes the atomic-precise, dynamic, and systems visualization of human membrane proteins and their endogenous modifiers. For years, bottom-up proteomics has grappled with removing and avoiding detergents, yet faltered at the therapeutic-pivotal membrane proteins, which have been tackled by classical approaches and are known for decades refractory to single-phase aqueous or organic denaturants. Hydrophobicity and aggregation commonly challenge tissue and cell lysates, biofluids, and enriched samples. Frequently, expected membrane proteins and peptides are not identified by shotgun bottom-up proteomics, let alone robust quantitation. This review argues the cause of this proteomic crisis is not detergents per se, but the choice of detergents. Recently, inclusion of compatible detergents for membrane protein extraction and digestion has revealed stark improvements in both quantitative and structural proteomics. This review analyzes detergent properties behind recent proteomic advances, and proposes that rational use of detergents may reconcile outstanding membrane proteomics dilemmas, enabling ultradeep coverage and minimal artifacts for robust protein and endogenous PTM measurements. The simplicity of detergent tools confers bottom-up membrane proteomics the sophistication toward precision medicine. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An exploration of NHS staff views on tuberculosis service delivery in Scottish NHS boards

PubMed Central

Spence, William

2013-01-01

Tuberculosis (TB) is a bacterial disease and major worldwide killer with an increased UK incidence rate. This study aimed to explore the views of National Health Service (NHS) staff on TB service delivery models of care in NHS boards across Scotland. Eighteen semi-structured interviews were conducted with 13 nurse specialists and five consultants in public health medicine (CPHM) across five Scottish NHS boards. Five main themes emerged and findings showed that: directly observed treatment (DOT) was provided only to patients assessed to be at high risk of poor treatment adherence; contact tracing was conducted by participating NHS boards but screening at ports was thought to be weak; all NHS boards implemented TB awareness campaigns for TB health professionals; three NHS boards conducted team meetings that monitored TB patient progress; participants believed that TB funding should be increased; contact tracing was routinely conducted by TB nurses. Improved TB screening at airports was recommended and a need for TB health education for high risk groups was identified. PMID:28989349

Family health nursing: the education programme for the WHO Europe Scottish Pilot.

PubMed

Murray, Ian

2004-06-01

This article outlines the development of the family health nurse (FNH) programme, which was delivered by the University of Stirling in the highlands and islands of Scotland as part of a World Health Organization European pilot project. An outline of the structure of the programme and its key features is described. The concept of the FHN emerged from the WHO's initiative to develop a practitioner who has the family as the organizing focus of their practice (WHO, 2000). An insight is provided into the experience of the first students to undergo this programme, along with a brief summary of the main findings of the external evaluation of both the education programme and the implementation of the role in the remote and rural communities of the highlands and islands of Scotland. Suggestions are made that will hopefully influence the second phase of this project that the Scottish Executive are supporting in an urban setting, which is due to begin in September 2004.

Managerial Performance Issues. Symposium 24. [AHRD Conference, 2001].

ERIC Educational Resources Information Center

2001

This document contains three papers on managerial performance issues. "Managerial Skill Requirements: Evidence from the Scottish Visitor Attraction Industry" (Sandra Watson, Martin McCracken) presents the findings from an exploratory study of those skills that managers in the Scottish visitor attraction sector considered most important…

Digitization of Microfilm: A Scottish Perspective.

ERIC Educational Resources Information Center

Lauder, John

1995-01-01

Discusses the Scottish Newspapers Microfilming Unit's interest in conversion of microfilm to digital technology. Concerns include cost, potential market, reliability of digital technology as a preservation medium, and the necessity to have both microfilm and digital formats for preservation. Solicits feedback and information from colleagues on the…

Patient Reported Outcome Measure of Spiritual Care as Delivered by Chaplains.

PubMed

Snowden, Austyn; Telfer, Iain

2017-01-01

Chaplains are employed by health organizations around the world to support patients in recognizing and addressing their spiritual needs. There is currently no generalizable measure of the impact of these interventions and so the clinical and strategic worth of chaplaincy is difficult to articulate. This article introduces the Scottish PROM, an original five-item patient reported outcome measure constructed specifically to address this gap. It describes the validation process from its conceptual grounding in the spiritual care literature through face and content validity cycles. It shows that the Scottish PROM is internally consistent and unidimensional. Responses to the Scottish PROM show strong convergent validity with responses to the Warwick and Edinburgh Mental Well-Being Scale, a generic well-being scale often used as a proxy for spiritual well-being. In summary, the Scottish PROM is fit for purpose. It measures the outcomes of spiritual care as delivered by chaplains in this study. This novel project introduces an essential and original breakthrough; the possibility of generalizable international chaplaincy research.

Most Scottish neurologists do not apply the 2010 McDonald criteria when diagnosing multiple sclerosis.

PubMed

Lumley, R; Davenport, R; Williams, A

2015-03-01

The diagnostic criteria for multiple sclerosis have evolved over time and currently the 2010 McDonald criteria are the most widely accepted. These criteria allow the diagnosis of multiple sclerosis to be made at the clinically isolated syndrome stage provided certain criteria are met on a single magnetic resonance brain scan. Our hypothesis was that neurologists in Scotland did not use these criteria routinely. We sent a SurveyMonkey questionnaire to all Scottish neurologists (consultants and trainees) regarding the diagnosis of multiple sclerosis. Our questionnaire response rate was 65/99 (66%). Most Scottish neurologists were aware of the criteria and 31/58 (53%) felt that they were using these routinely. However, in a clinical vignette designed to test the application of these criteria, only 5/57 (9%) of neurologists appeared to use them. Scottish neurologists' use of the 2010 McDonald criteria for diagnosis of multiple sclerosis varies from practitioners' perception of their use of these criteria.

Distribution of apolipoprotein E alleles in a Scottish healthy newborn population.

PubMed

Becher, J-C; Bell, J E; McIntosh, N; Keeling, J W

2005-01-01

The different alleles of the human apolipoprotein E polymorphism, ApoE epsilon2, epsilon3, epsilon4, have important implications for systemic lipid metabolism, immunological function and for the brain in maintenance and in response to injury. Few studies have focussed on their role in early life. The ApoE alleles and genotypes were ascertained in the cord blood of 371 full-term and normal Scottish newborn infants using PCR methodology. The results were compared to previously published data for Scottish adults in late middle age. There was a marginally significant over-representation of epsilon4 and under-representation of epsilon3 alleles in healthy infants as compared with adults. Inspection of the individual genotypes confirms the over-representation of ApoE 4/4 and 2/4 with a reduction in ApoE 2/3 and 3/3 when compared with Scottish adults. Although these results may have occurred by chance, the ApoE epsilon4 allele may confer an increased risk of premature death. Copyright (c) 2005 S. Karger AG, Basel.

Parasites, proteomes and systems: has Descartes' clock run out of time?

PubMed

Wastling, J M; Armstrong, S D; Krishna, R; Xia, D

2012-08-01

Systems biology aims to integrate multiple biological data types such as genomics, transcriptomics and proteomics across different levels of structure and scale; it represents an emerging paradigm in the scientific process which challenges the reductionism that has dominated biomedical research for hundreds of years. Systems biology will nevertheless only be successful if the technologies on which it is based are able to deliver the required type and quality of data. In this review we discuss how well positioned is proteomics to deliver the data necessary to support meaningful systems modelling in parasite biology. We summarise the current state of identification proteomics in parasites, but argue that a new generation of quantitative proteomics data is now needed to underpin effective systems modelling. We discuss the challenges faced to acquire more complete knowledge of protein post-translational modifications, protein turnover and protein-protein interactions in parasites. Finally we highlight the central role of proteome-informatics in ensuring that proteomics data is readily accessible to the user-community and can be translated and integrated with other relevant data types.

Parasites, proteomes and systems: has Descartes’ clock run out of time?

PubMed Central

WASTLING, J. M.; ARMSTRONG, S. D.; KRISHNA, R.; XIA, D.

2012-01-01

SUMMARY Systems biology aims to integrate multiple biological data types such as genomics, transcriptomics and proteomics across different levels of structure and scale; it represents an emerging paradigm in the scientific process which challenges the reductionism that has dominated biomedical research for hundreds of years. Systems biology will nevertheless only be successful if the technologies on which it is based are able to deliver the required type and quality of data. In this review we discuss how well positioned is proteomics to deliver the data necessary to support meaningful systems modelling in parasite biology. We summarise the current state of identification proteomics in parasites, but argue that a new generation of quantitative proteomics data is now needed to underpin effective systems modelling. We discuss the challenges faced to acquire more complete knowledge of protein post-translational modifications, protein turnover and protein-protein interactions in parasites. Finally we highlight the central role of proteome-informatics in ensuring that proteomics data is readily accessible to the user-community and can be translated and integrated with other relevant data types. PMID:22828391

The proteomic profile of hair damage.

PubMed

Sinclair, R; Flagler, M J; Jones, L; Rufaut, N; Davis, M G

2012-06-01

Monilethrix is a congenital hair shaft disorder with associated fragility. Many of the changes seen in monilethrix hair on light microscopy and scanning electron microscopy are also seen in hair weathering and cosmetic damage to hair. We used monilethrix as a model to investigate the relationship between hair protein structure and hair strength and resistance to cosmetic insult. We applied proteomic techniques to identify novel peptide damage markers for chemical oxidative damage to hair. The findings suggest that specific sites in the protein structure of hair are targeted during oxidative damage from bleaching, a unique insight into how chemical damage compromises the structural integrity of the hair shaft at the molecular level. Applying proteomics to the study of congenital and acquired hair shaft disorders can deliver new insights into hair damage and novel strategies to strengthen hair. © 2012 The Authors. BJD © 2012 British Association of Dermatologists.

The "Curriculum for Excellence": A Major Change for Scottish Science Education

ERIC Educational Resources Information Center

Brown, Sally

2014-01-01

The Curriculum for Excellence and new National Qualifications offer innovative reform, based on widely supported ideas and aims, for Scottish preschool, primary and secondary education levels. "Objectives and syllabuses" for science are replaced by "experiences and outcomes". Most strikingly, central prescription makes way for…

Collaboration between Science and Religious Education Teachers in Scottish Secondary Schools

ERIC Educational Resources Information Center

Hall, Stuart; McKinney, Stephen; Lowden, Kevin; Smith, Marjorie; Beaumont, Paul

2014-01-01

The article reports on quantitative research that examines: (1) the current practice in collaboration; and (2) potential for collaboration between Science and Religious Education teachers in a large sample of Scottish secondary schools. The authors adopt and adapt three models ("conflict"; "concordat" and…

Bright Ideas, Creative People, Teamwork, and Money: Developing Courseware for Teaching Scottish History.

ERIC Educational Resources Information Center

Munro, R. K.; Hillis, P. L. M.

1996-01-01

Describes three hypermedia databases designed to support secondary education classes in Scottish history. The databases contain mostly 19th-century census information with links to subjects such as fashion, education, and entertainment. Interactive interfaces allow students to create original research applications. (MJP)

Student Engagement in the Scottish Quality Enhancement Framework

ERIC Educational Resources Information Center

Gvaramadze, Irakli

2011-01-01

The research addressed the interplay of student engagement and quality enhancement mechanisms in the Scottish higher education system. The paper demonstrates increasing focus on student learning, learning experience and high-quality learning in the current quality enhancement approaches. The student-university coproduction model is used to…

The Scottish Centre for Mathematics, Science and Technical Education

ERIC Educational Resources Information Center

Sandercock, E. R.

1977-01-01

The Centre's functions are described. A flow diagram, developed for the Scottish Integrated Science Course, showing a modular approach to science for mixed ability or low ability students is given. This course is intended for students in their first two years of secondary education. (AJ)

'Not our war, not our country': contents and contexts of Scottish political rhetoric and popular understandings during the invasion of Iraq.

PubMed

Elcheroth, Guy; Reicher, Steve

2014-03-01

Recent research has questioned the traditional assumption that populations inevitably rally round their national leaders in times of war and suggested instead that whether this occurs depends upon political communication and mass media coverage. In this study, we provide systematic analysis of the debate in Scotland over the invasion of Iraq in 2003. We examine how the conflict was construed as either for or against the national interest, and how the way this is done is linked to different dimensions of context. First, we provide a mixed-methods analysis of debates in the Scottish Parliament. We show that anti-war speakers from Scottish separatist parties map opposition to the war onto a series of collectively consistent and temporarily flexible categorical oppositions, starting with a familiar antinomy between Scottish people and British rulers (before the invasion), and then shifting to broader oppositions between subjugated people and imperial powers (after the invasion). By contrast, speakers from other parties appear less consistent and less flexible in the nature of their arguments. Second, we examine the opinions of a population sample on the war, how these opinions relate to understandings of Scottish identity and how the media context is pivotal in the translation of anti-war opinions into votes for separatist/anti-war political parties. © 2013 The British Psychological Society.

Proteobionics: biomimetics in proteomics.

PubMed

Sommer, Andrei P; Gheorghiu, Eleonora

2006-03-01

Proteomics was established 10 years ago by the analysis of microbial genomes via their protein complement or proteome. Bionics is an ancient art, which converts structures optimized by nature into advanced technical products. Previously, we analyzed survival modalities in nanobacteria and converted the interplay between survival-oriented protein functions and nanoscale mineral shells into models for advanced drug delivery. Exploiting protein functions observed in nature to design biomedical products and therapies could be named proteobionics. Here, we present examples for this new branch of nanoproteomics.

Less is More: Membrane Protein Digestion Beyond Urea-Trypsin Solution for Next-level Proteomics.

PubMed

Zhang, Xi

2015-09-01

The goal of next-level bottom-up membrane proteomics is protein function investigation, via high-coverage high-throughput peptide-centric quantitation of expression, modifications and dynamic structures at systems scale. Yet efficient digestion of mammalian membrane proteins presents a daunting barrier, and prevalent day-long urea-trypsin in-solution digestion proved insufficient to reach this goal. Many efforts contributed incremental advances over past years, but involved protein denaturation that disconnected measurement from functional states. Beyond denaturation, the recent discovery of structure/proteomics omni-compatible detergent n-dodecyl-β-d-maltopyranoside, combined with pepsin and PNGase F columns, enabled breakthroughs in membrane protein digestion: a 2010 DDM-low-TCEP (DLT) method for H/D-exchange (HDX) using human G protein-coupled receptor, and a 2015 flow/detergent-facilitated protease and de-PTM digestions (FDD) for integrative deep sequencing and quantitation using full-length human ion channel complex. Distinguishing protein solubilization from denaturation, protease digestion reliability from theoretical specificity, and reduction from alkylation, these methods shifted day(s)-long paradigms into minutes, and afforded fully automatable (HDX)-protein-peptide-(tandem mass tag)-HPLC pipelines to instantly measure functional proteins at deep coverage, high peptide reproducibility, low artifacts and minimal leakage. Promoting-not destroying-structures and activities harnessed membrane proteins for the next-level streamlined functional proteomics. This review analyzes recent advances in membrane protein digestion methods and highlights critical discoveries for future proteomics. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Ionotropic AMPA-type glutamate and metabotropic GABAB receptors: determining cellular physiology by proteomes.

PubMed

Bettler, Bernhard; Fakler, Bernd

2017-08-01

Ionotropic AMPA-type glutamate receptors and G-protein-coupled metabotropic GABA B receptors are key elements of neurotransmission whose cellular functions are determined by their protein constituents. Over the past couple of years unbiased proteomic approaches identified comprehensive sets of protein building blocks of these two types of neurotransmitter receptors in the brain (termed receptor proteomes). This provided the opportunity to match receptor proteomes with receptor physiology and to study the structural organization, regulation and function of native receptor complexes in an unprecedented manner. In this review we discuss the principles of receptor architecture and regulation emerging from the functional characterization of the proteomes of AMPA and GABA B receptors. We also highlight progress in unraveling the role of unexpected protein components for receptor physiology. Copyright © 2017 Elsevier Ltd. All rights reserved.

Covering complete proteomes with X-ray structures: A current snapshot

DOE PAGES

Mizianty, Marcin J.; Fan, Xiao; Yan, Jing; ...

2014-10-23

Structural genomics programs have developed and applied structure-determination pipelines to a wide range of protein targets, facilitating the visualization of macromolecular interactions and the understanding of their molecular and biochemical functions. The fundamental question of whether three-dimensional structures of all proteins and all functional annotations can be determined using X-ray crystallography is investigated. A first-of-its-kind large-scale analysis of crystallization propensity for all proteins encoded in 1953 fully sequenced genomes was performed. It is shown that current X-ray crystallographic knowhow combined with homology modeling can provide structures for 25% of modeling families (protein clusters for which structural models can be obtainedmore » through homology modeling), with at least one structural model produced for each Gene Ontology functional annotation. The coverage varies between superkingdoms, with 19% for eukaryotes, 35% for bacteria and 49% for archaea, and with those of viruses following the coverage values of their hosts. It is shown that the crystallization propensities of proteomes from the taxonomic superkingdoms are distinct. The use of knowledge-based target selection is shown to substantially increase the ability to produce X-ray structures. It is demonstrated that the human proteome has one of the highest attainable coverage values among eukaryotes, and GPCR membrane proteins suitable for X-ray structure determination were determined.« less

Student-Adult Mentoring Relationships: Experiences from a Scottish School-Based Programme

ERIC Educational Resources Information Center

Mtika, Peter; Payne, Frances

2014-01-01

Background: This article reports on a mentoring programme which was implemented in selected Scottish secondary schools with the view to supporting students with school work, transition to further education/higher education, careers, and interpersonal skills. Mentoring students can enhance their academic, social, career and other outcomes.…

Integration of a Miniaturized Conductivity Sensor into an Animal-borne Instrument

DTIC Science & Technology

2014-09-30

animal-borne instrument Lars Boehme Sea Mammal Research Unit Scottish Oceans Institute University of St Andrews St Andrews, KY16 8LB United...NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) University of St Andrews, Scottish Oceans Institute,Sea Mammal Research Unit,St Andrews

The Wider View

ERIC Educational Resources Information Center

Lawrence, Liz

2010-01-01

In this article, the author talks about Primary Science Committee's (PSC) joint meeting with members of the Scottish Primary Group in Edinburgh. The remit of the group is to advise on primary matters, develop primary aspects of Scottish Region's Annual Conference and run primary-focused continuing professional development (CPD) events as part of…

"To Form Citizens": Scottish Students, Governance and Politics, 1884-1948

ERIC Educational Resources Information Center

Macdonald, Catriona M. M.

2009-01-01

Citizenship was not a straightforward concern for Scottish university students between 1884 and 1948 and tended to express itself in multiple and often competing allegiances. Despite students being empowered to elect a Rector, and their role in university governance being accorded statutory recognition through the Students' Representative…

Learners with Profound and Complex Needs in Scotland's Colleges

ERIC Educational Resources Information Center

Her Majesty's Inspectorate of Education, 2009

2009-01-01

The Scottish Further and Higher Education Funding Council's (SFC) Corporate Plan (2009-12) makes clear its commitment to learners with profound and complex needs. Under "Outcome 2 Access, Inclusion and Progression" it states: "we will work with the Scottish Government, colleges and other stakeholders to ensure that appropriate…

Gaelic Singing and Oral Tradition

ERIC Educational Resources Information Center

Sheridan, Mark; MacDonald, Iona; Byrne, Charles G.

2011-01-01

A recent report by UNESCO placed Scots Gaelic on a list of 2500 endangered languages highlighting the perilous state of a key cornerstone of Scottish culture. Scottish Gaelic song, poems and stories have been carried through oral transmission for many centuries reflecting the power of indigenous peoples to preserve cultural heritage from…

Managing Change in Small Scottish Primary Schools. SCRE Research Report Series.

ERIC Educational Resources Information Center

Wilson, Valerie; McPake, Joanna

This report describes Scottish research on ways in which headteachers in small primary schools managed mandated changes. The research focused on implementation of four recent major initiatives: 5-14 Curriculum Guidelines, School Development Planning, Staff Development and Appraisal, and Devolved School Management. Research methods included a…

National and Scottish Vocational Qualifications: Early Indications of Employers' Take-up and Use.

ERIC Educational Resources Information Center

Callender, C.; And Others

A study examined British employers' adoption of National Vocational Qualifications and Scottish Vocational Qualifications (NVQ/SVQs) and the occupational standards underpinning them. Data regarding current/projected use of the NVQ/SVQs and their perceived costs, benefits, and difficulties of implementation were collected from the following:…

Project-Based Learning in Scottish Prisons

ERIC Educational Resources Information Center

Sams, Kirsten

2014-01-01

The article describes the development of a project-based approach to learning in seven Scottish prisons. It argues that the project-based approach is ideally suited to prison education due to its flexibility and ability to enrich the relatively narrow prison curriculum and create meaningful links with wider society, reducing the isolation of…

Scottish Visitor Attractions: Managerial Competence Requirements

ERIC Educational Resources Information Center

Watson, Sandra; McCracken, Martin; Hughes, Moira

2004-01-01

This paper presents the findings from a study into managerial competence in the Scottish visitor attraction sector. It provides an insight into the range, diversity and perceived importance of current and future competences highlighting differences based on gender, age, size, level of training and location. Although the main findings reveal a…

Managing Change in Small Scottish Primary Schools: Is There a Small School Management Style?

ERIC Educational Resources Information Center

Wilson, Valerie; McPake, Joanna

2000-01-01

Identifies management activities and strategies used by 863 heads of small Scottish schools to implement 4 major national initiatives during the past decade. Headteachers valued teamwork and employed a "plan-implement-review" strategy involving a quick audit, realistic planning for achievable targets, inclusive implementation, and…

SMEs and Barriers to Skill Development: A Scottish Perspective.

ERIC Educational Resources Information Center

Lange, Thomas; Ottens, Melanie; Taylor, Andrea

2000-01-01

Analysis of Scottish small and medium-sized enterprises reveals that small business culture is a significant barrier to skill development. Other barriers include awareness, finance, and access to training. A welter of recent policy initiatives has added to a state of confusion about the role of training. (SK)

Drowning or Waving? Coping Strategies among Scottish Head Teachers

ERIC Educational Resources Information Center

MacBeath, John; O'Brien, Jim; Gronn, Peter

2012-01-01

In the year 2007 in Scotland, in common with countries elsewhere in the world, the difficulty of recruiting high-calibre school leaders was becoming an increasing concern. The recruitment and retention study, commissioned by the Scottish Government and undertaken by three universities (Cambridge, Edinburgh and Glasgow), was charged with exploring…

PubMed Central

Castagnola, M.; Scarano, E.; Messana, I.; Cabras, T.; Iavarone, F.; Di Cintio, G.; Fiorita, A.; De Corso, E.; Paludetti, G.

2017-01-01

SUMMARY Saliva testing is a non-invasive and inexpensive test that can serve as a source of information useful for diagnosis of disease. As we enter the era of genomic technologies and –omic research, collection of saliva has increased. Recent proteomic platforms have analysed the human salivary proteome and characterised about 3000 differentially expressed proteins and peptides: in saliva, more than 90% of proteins in weight are derived from the secretion of three couples of "major" glands; all the other components are derived from minor glands, gingival crevicular fluid, mucosal exudates and oral microflora. The most common aim of proteomic analysis is to discriminate between physiological and pathological conditions. A proteomic protocol to analyze the whole saliva proteome is not currently available. It is possible distinguish two type of proteomic platforms: top-down proteomics investigates intact naturally-occurring structure of a protein under examination; bottom-up proteomics analyses peptide fragments after pre-digestion (typically with trypsin). Because of this heterogeneity, many different biomarkers may be proposed for the same pathology. The salivary proteome has been characterised in several diseases: oral squamous cell carcinoma and oral leukoplakia, chronic graft-versus-host disease Sjögren's syndrome and other autoimmune disorders such as SAPHO, schizophrenia and bipolar disorder, and genetic diseases like Down's Syndrome and Wilson disease. The results of research reported herein suggest that in the near future human saliva will be a relevant diagnostic fluid for clinical diagnosis and prognosis. PMID:28516971

The proteome: structure, function and evolution

PubMed Central

Fleming, Keiran; Kelley, Lawrence A; Islam, Suhail A; MacCallum, Robert M; Muller, Arne; Pazos, Florencio; Sternberg, Michael J.E

2006-01-01

This paper reports two studies to model the inter-relationships between protein sequence, structure and function. First, an automated pipeline to provide a structural annotation of proteomes in the major genomes is described. The results are stored in a database at Imperial College, London (3D-GENOMICS) that can be accessed at www.sbg.bio.ic.ac.uk. Analysis of the assignments to structural superfamilies provides evolutionary insights. 3D-GENOMICS is being integrated with related proteome annotation data at University College London and the European Bioinformatics Institute in a project known as e-protein (http://www.e-protein.org/). The second topic is motivated by the developments in structural genomics projects in which the structure of a protein is determined prior to knowledge of its function. We have developed a new approach PHUNCTIONER that uses the gene ontology (GO) classification to supervise the extraction of the sequence signal responsible for protein function from a structure-based sequence alignment. Using GO we can obtain profiles for a range of specificities described in the ontology. In the region of low sequence similarity (around 15%), our method is more accurate than assignment from the closest structural homologue. The method is also able to identify the specific residues associated with the function of the protein family. PMID:16524832

A Statistical Selection Strategy for Normalization Procedures in LC-MS Proteomics Experiments through Dataset Dependent Ranking of Normalization Scaling Factors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Webb-Robertson, Bobbie-Jo M.; Matzke, Melissa M.; Jacobs, Jon M.

2011-12-01

Quantification of LC-MS peak intensities assigned during peptide identification in a typical comparative proteomics experiment will deviate from run-to-run of the instrument due to both technical and biological variation. Thus, normalization of peak intensities across a LC-MS proteomics dataset is a fundamental step in pre-processing. However, the downstream analysis of LC-MS proteomics data can be dramatically affected by the normalization method selected . Current normalization procedures for LC-MS proteomics data are presented in the context of normalization values derived from subsets of the full collection of identified peptides. The distribution of these normalization values is unknown a priori. If theymore » are not independent from the biological factors associated with the experiment the normalization process can introduce bias into the data, which will affect downstream statistical biomarker discovery. We present a novel approach to evaluate normalization strategies, where a normalization strategy includes the peptide selection component associated with the derivation of normalization values. Our approach evaluates the effect of normalization on the between-group variance structure in order to identify candidate normalization strategies that improve the structure of the data without introducing bias into the normalized peak intensities.« less

Proteomic-based comparison between populations of the Great Scallop, Pecten maximus.

PubMed

Artigaud, Sébastien; Lavaud, Romain; Thébault, Julien; Jean, Fred; Strand, Oivind; Strohmeier, Tore; Milan, Massimo; Pichereau, Vianney

2014-06-13

Comparing populations residing in contrasting environments is an efficient way to decipher how organisms modulate their physiology. Here we present the proteomic signatures of two populations in a non-model marine species, the great scallop Pecten maximus, living in the northern (Hordaland, Norway) and in the center (Brest, France) of this species' latitudinal distribution range. The results showed 38 protein spots significantly differentially accumulated in mantle tissues between the two populations. We could unambiguously identify 11 of the protein spots by Maldi TOF-TOF mass spectrometry. Eight proteins corresponded to different isoforms of actin, two were identified as filamin, another protein related to the cytoskeleton structure, and one was the protease elastase. Our results suggest that scallops from the two populations assayed may modulate their cytoskeleton structures through regulation of intracellular pools of actin and filamin isoforms to better adapt to their environment. Marine mollusks are non-model organisms that have been poorly studied at the proteomic level, and this article is the first studying the great scallop (P. maximus) at this level. Furthermore, it addresses population proteomics, a new promising field, especially in environmental sciences. This article is part of a Special Issue entitled: Proteomics of non-model organisms. Copyright © 2014 Elsevier B.V. All rights reserved.

How commercial and non-commercial swine producers move pigs in Scotland: a detailed descriptive analysis

PubMed Central

2014-01-01

Background The impact of non-commercial producers on disease spread via livestock movement is related to their level of interaction with other commercial actors within the industry. Although understanding these relationships is crucial in order to identify likely routes of disease incursion and transmission prior to disease detection, there has been little research in this area due to the difficulties of capturing movements of small producers with sufficient resolution. Here, we used the Scottish Livestock Electronic Identification and Traceability (ScotEID) database to describe the movement patterns of different pig production systems which may affect the risk of disease spread within the swine industry. In particular, we focused on the role of small pig producers. Results Between January 2012 and May 2013, 23,169 batches of pigs were recorded moving animals between 2382 known unique premises. Although the majority of movements (61%) were to a slaughterhouse, the non-commercial and the commercial sectors of the Scottish swine industry coexist, with on- and off-movement of animals occurring relatively frequently. For instance, 13% and 4% of non-slaughter movements from professional producers were sent to a non-assured commercial producer or to a small producer, respectively; whereas 43% and 22% of movements from non-assured commercial farms were sent to a professional or a small producer, respectively. We further identified differences between producer types in several animal movement characteristics which are known to increase the risk of disease spread. Particularly, the distance travelled and the use of haulage were found to be significantly different between producers. Conclusions These results showed that commercial producers are not isolated from the non-commercial sector of the Scottish swine industry and may frequently interact, either directly or indirectly. The observed patterns in the frequency of movements, the type of producers involved, the distance travelled and the use of haulage companies provide insights into the structure of the Scottish swine industry, but also highlight different features that may increase the risk of infectious diseases spread in both Scotland and the UK. Such knowledge is critical for developing more robust biosecurity and surveillance plans and better preparing Scotland against incursions of emerging swine diseases. PMID:24965915

How commercial and non-commercial swine producers move pigs in Scotland: a detailed descriptive analysis.

PubMed

Porphyre, Thibaud; Boden, Lisa A; Correia-Gomes, Carla; Auty, Harriet K; Gunn, George J; Woolhouse, Mark E J

2014-06-25

The impact of non-commercial producers on disease spread via livestock movement is related to their level of interaction with other commercial actors within the industry. Although understanding these relationships is crucial in order to identify likely routes of disease incursion and transmission prior to disease detection, there has been little research in this area due to the difficulties of capturing movements of small producers with sufficient resolution. Here, we used the Scottish Livestock Electronic Identification and Traceability (ScotEID) database to describe the movement patterns of different pig production systems which may affect the risk of disease spread within the swine industry. In particular, we focused on the role of small pig producers. Between January 2012 and May 2013, 23,169 batches of pigs were recorded moving animals between 2382 known unique premises. Although the majority of movements (61%) were to a slaughterhouse, the non-commercial and the commercial sectors of the Scottish swine industry coexist, with on- and off-movement of animals occurring relatively frequently. For instance, 13% and 4% of non-slaughter movements from professional producers were sent to a non-assured commercial producer or to a small producer, respectively; whereas 43% and 22% of movements from non-assured commercial farms were sent to a professional or a small producer, respectively. We further identified differences between producer types in several animal movement characteristics which are known to increase the risk of disease spread. Particularly, the distance travelled and the use of haulage were found to be significantly different between producers. These results showed that commercial producers are not isolated from the non-commercial sector of the Scottish swine industry and may frequently interact, either directly or indirectly. The observed patterns in the frequency of movements, the type of producers involved, the distance travelled and the use of haulage companies provide insights into the structure of the Scottish swine industry, but also highlight different features that may increase the risk of infectious diseases spread in both Scotland and the UK. Such knowledge is critical for developing more robust biosecurity and surveillance plans and better preparing Scotland against incursions of emerging swine diseases.

A perspective on extracellular vesicles proteomics

NASA Astrophysics Data System (ADS)

Rosa-Fernandes, Livia; Rocha, Victória Bombarda; Carregari, Victor Corasolla; Urbani, Andrea; Palmisano, Giuseppe

2017-11-01

Increasing attention has been given to secreted extracellular vesicles (EVs) in the past decades, especially in the portrayal of their molecular cargo and role as messengers in both homeostasis and pathophysiological conditions. This review presents the state-of-the-art proteomic technologies to identify and quantify EVs proteins along with their PTMs, interacting partners and structural details. The rapid growth of mass spectrometry-based analytical strategies for protein sequencing, PTMs and structural characterization has improved the level of molecular details that can be achieve from limited amount of EVs isolated from different biological sources. Here we will provide a perspective view on the achievements and challenges on EVs proteome characterization using mass spectrometry. A detailed bioinformatics approach will help us to picture the molecular fingerprint of EVs and understand better their pathophysiological function.

Callanish, a Scottish Stonehenge: A group of standing stones was used by Stone Age man to mark the seasons and perhaps to predict eclipse seasons.

PubMed

Hawkins, G S

1965-01-08

On the basis of the stone record it appears that the Callanish people were as precise as the Stonehengers in setting up their megalithic structure, but not as scientifically advanced. Callanish is, however, a structure that could have been used much as Stonehenge was. It would be interesting to obtain a date, by the radiocarbon method, for the peat in the area of Callanish, to determine how much older, or more recent, than Stonehenge this structure is. Perhaps the knowledge gained at Callanish was later used in the design of Stonehenge.

Does water stress promote the proteome-wide adjustment of intrinsically disordered proteins in plants?

PubMed

Zamora-Briseño, Jesús Alejandro; Reyes-Hernández, Sandi Julissa; Zapata, Luis Carlos Rodríguez

2018-06-02

Plant response to water stress involves the activation of mechanisms expected to help them cope with water scarcity. Among these mechanisms, proteome-wide adjustment is well known. This includes actions to save energy, protect cellular and molecular components, and maintain vital functions of the cell. Intrinsically disordered proteins, which are proteins without a rigid three-dimensional structure, are seen as emerging multifunctional cellular components of proteomes. They are highly abundant in eukaryotic proteomes, and numerous functions for these proteins have been proposed. Here, we discuss several reasons why the collection of intrinsically disordered proteins in a proteome (disordome) could be subjected to an active regulation during conditions of water scarcity in plants. We also discuss the potential misinterpretations of disordome content estimations made so far due to bias-prone data and the need for reliable analysis based on experimental data in order to acknowledge the plasticity nature of the disordome.

Automation, parallelism, and robotics for proteomics.

PubMed

Alterovitz, Gil; Liu, Jonathan; Chow, Jijun; Ramoni, Marco F

2006-07-01

The speed of the human genome project (Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C. et al., Nature 2001, 409, 860-921) was made possible, in part, by developments in automation of sequencing technologies. Before these technologies, sequencing was a laborious, expensive, and personnel-intensive task. Similarly, automation and robotics are changing the field of proteomics today. Proteomics is defined as the effort to understand and characterize proteins in the categories of structure, function and interaction (Englbrecht, C. C., Facius, A., Comb. Chem. High Throughput Screen. 2005, 8, 705-715). As such, this field nicely lends itself to automation technologies since these methods often require large economies of scale in order to achieve cost and time-saving benefits. This article describes some of the technologies and methods being applied in proteomics in order to facilitate automation within the field as well as in linking proteomics-based information with other related research areas.

Drought-Responsive Mechanisms in Plant Leaves Revealed by Proteomics.

PubMed

Wang, Xiaoli; Cai, Xiaofeng; Xu, Chenxi; Wang, Quanhua; Dai, Shaojun

2016-10-18

Plant drought tolerance is a complex trait that requires a global view to understand its underlying mechanism. The proteomic aspects of plant drought response have been extensively investigated in model plants, crops and wood plants. In this review, we summarize recent proteomic studies on drought response in leaves to reveal the common and specialized drought-responsive mechanisms in different plants. Although drought-responsive proteins exhibit various patterns depending on plant species, genotypes and stress intensity, proteomic analyses show that dominant changes occurred in sensing and signal transduction, reactive oxygen species scavenging, osmotic regulation, gene expression, protein synthesis/turnover, cell structure modulation, as well as carbohydrate and energy metabolism. In combination with physiological and molecular results, proteomic studies in leaves have helped to discover some potential proteins and/or metabolic pathways for drought tolerance. These findings provide new clues for understanding the molecular basis of plant drought tolerance.

Drought-Responsive Mechanisms in Plant Leaves Revealed by Proteomics

PubMed Central

Wang, Xiaoli; Cai, Xiaofeng; Xu, Chenxi; Wang, Quanhua; Dai, Shaojun

2016-01-01

Plant drought tolerance is a complex trait that requires a global view to understand its underlying mechanism. The proteomic aspects of plant drought response have been extensively investigated in model plants, crops and wood plants. In this review, we summarize recent proteomic studies on drought response in leaves to reveal the common and specialized drought-responsive mechanisms in different plants. Although drought-responsive proteins exhibit various patterns depending on plant species, genotypes and stress intensity, proteomic analyses show that dominant changes occurred in sensing and signal transduction, reactive oxygen species scavenging, osmotic regulation, gene expression, protein synthesis/turnover, cell structure modulation, as well as carbohydrate and energy metabolism. In combination with physiological and molecular results, proteomic studies in leaves have helped to discover some potential proteins and/or metabolic pathways for drought tolerance. These findings provide new clues for understanding the molecular basis of plant drought tolerance. PMID:27763546

The Scottish Council for Research in Education: Fifty-Fifth Annual Report 1982-83.

ERIC Educational Resources Information Center

Scottish Council for Research in Education.

Reports are given on activities of the Scottish Council for Research in Education. Included are the Chairman's Report and those of the Finance and General Purpose Committee, Communications Committee, and the Research Committee. Summaries are presented of research projects involving: (1) primary school teaching strategies; (2) students' awareness…

The Scottish Credit and Qualifications Framework: What's Academic Practice Got to Do with It?

ERIC Educational Resources Information Center

Fernie, Scott; Pilcher, Nick; Smith, Karen L.

2014-01-01

National Qualifications Frameworks (NQF) are a globally established and expanding phenomenon. They are increasingly merging and being mapped onto meta-qualifications frameworks. One key NQF in both these roles is the Scottish Credit and Qualifications Framework (SCQF). Much research categorises the different types of NQF, details their success and…

Closing the Attainment Gap--A Realistic Proposition or an Elusive Pipe-Dream?

ERIC Educational Resources Information Center

Mowat, Joan Gaynor

2018-01-01

The attainment gap associated with socio-economic status is an international problem that is highly resistant to change. This conceptual paper critiques the drive by the Scottish Government to address the attainment gap through the Scottish Attainment Challenge and the National Improvement Framework. It draws upon a range of theoretical…

The SERA Lecture 2013: Scottish Research in a Global Context--Dependence, Independence or Interdependence?

ERIC Educational Resources Information Center

Menter, Ian

2014-01-01

Educational research in Scotland has a very distinguished history and has made a major contribution in several aspects of methodology, not least in the relationships between researchers, policymakers and practitioners. The paper considers the Scottish contribution to the development of educational research past, present and future and the…

Preservice Principals' Post-Internship Concerns about Becoming a Principal: America and Scotland in Review

ERIC Educational Resources Information Center

Hines, Mack T., III

2008-01-01

The purpose of this study was to compare American and Scottish preservice principals' post-internship concerns about becoming a principal. The survey findings for this study showed that overall American preservice principals were more concerned about becoming principals than their Scottish preservice counterparts. Based on the groups' discussion…

Assured Optimism in a Scottish Girls' School: Habitus and the (Re)production of Global Privilege

ERIC Educational Resources Information Center

Forbes, Joan; Lingard, Bob

2015-01-01

This paper examines how high levels of social-cultural connectedness and academic excellence, inflected by gender and social class, constitute a particular school habitus of "assured optimism" at an elite Scottish girls' school. In Bourdieuian terms, Dalrymple is a "forcing ground" for the "intense cultivation" of a…

Feeling the Strain: An Overview of the Literature on Teachers' Stress.

ERIC Educational Resources Information Center

Wilson, Valerie

The Scottish Council for Research in Education (SCRE) reviewed the literature on teacher stress, examining what stress is, causes and effects of stress in teaching, how teaching compares with other professions, what Scottish research says, and how teachers cope with stress. Stress has increasingly acquired a negative connotation, implying…

Equity and Lifelong Learning: Lessons from Workplace Learning in Scottish SMEs

ERIC Educational Resources Information Center

Riddell, Sheila; Ahlgren, Linda; Weedon, Elisabet

2009-01-01

Workplace learning is identified by UK and Scottish governments as an important means of achieving social mobility, and therefore producing a more equal society. However, there appears to be a patchwork of provision and funding arrangements, making it difficult for employers and employees to identify suitable routes. Analysis of large scale survey…

Additional Support Needs Policy in Scotland: Challenging or Reinforcing Social Inequality?

ERIC Educational Resources Information Center

Riddell, Sheila; Weedon, Elisabet

2016-01-01

This paper focuses on Scottish policy on additional support needs and its material outcomes. The central question addressed is the extent to which the Scottish additional support needs system undermines or reinforces existing social and economic inequalities. Administrative data highlight the inflation of the additional support needs category,…

Scottish Schools Science Equipment Research Centre, Bulletin No. 64, July, 1973.

ERIC Educational Resources Information Center

Scottish Schools Science Equipment Research Centre, Edinburgh.

This bulletin of the Scottish Schools Science Equipment Research Centre provides information to teachers on a variety of topics relating to the use of equipment in science instruction. The introductory remarks deal with an assessment of electronic calculators suitable for use in schools. The section entitled "Physics Notes" lists surplus…

NETWORK. A History of the Scottish Telephone Referral Service.

ERIC Educational Resources Information Center

Smith, Vernon

Since its beginnings in 1974 as an outgrowth of the BBC Adult Literacy project, NETWORK SCOTLAND LTD (formerly the Scottish Telephone Referral Service) has grown to play a key role in the provision of broadcast support and educational information services in the United Kingdom. The referral service was originally established to provide a mechanism…

Scottish School Leavers' Survey: Entrants to Higher Education.

ERIC Educational Resources Information Center

Tinklin, Teresa; Raffe, David

This report describes trends and patterns in school-leaver entry to higher education in Scotland. (School-leaver entrants to higher education are those who leave school and start higher education in the same year, or direct entrants.) The report uses data from the Scottish School Leavers' Survey (SSLS), a biennial sample survey of school leavers…

Scottish Schools Science Equipment Research Centre Bulletin No. 55.

ERIC Educational Resources Information Center

1972

Instructions for the construction of the following apparatus for the secondary school science laboratory are included in this issue of the Scottish Schools Science Equipment Research Centre Bulletin: a cheap water purifier using an expendable deionizer can; a simple amplifier suitable for detecting or displaying D. C. currents of 1 microamp or…

Liquid Modernity: Exploring the Research Contract Nexus within Contemporary Scottish Political Culture

ERIC Educational Resources Information Center

Holligan, Chris

2013-01-01

This paper contributes to our understanding of a supposed free-market in research, where knowledge-transfer is to government, which then brokers the evidence into professional fields. Education research contracts are put out to tender by Scottish Government and a constellation of factors constructing this phenomenon has epistemological and…

Changes and Challenges: Key Issues for Scottish Rural Schools and Communities

ERIC Educational Resources Information Center

Dowling, Jennie

2009-01-01

Education in rural Scottish schools has changed rapidly over the past 15 years. These changes include the implementation of national curriculum and assessment guidelines, increased parental influence and a shift from local authority based management to more locally based schemes. During the 1990s, research in the field focused largely on learning…

Widening Access to Scottish Higher Education: Unresolved Issues and Future Challenges

ERIC Educational Resources Information Center

Riddell, Sheila

2016-01-01

Despite the Scottish Government's frequent affirmation of its commitment to social justice principles, there has of late been a recognition of the need for firmer action to tackle the social class gap in higher education participation, reflecting wider social inequalities in Scotland. In a recent policy statement, Angela Constance, Cabinet…

Delivering Sustainable Practice? A Case Study of the Scottish Active Schools Programme

ERIC Educational Resources Information Center

Reid, Gavin

2009-01-01

Since 1999, concerns about Scotland's future health and economic performance have profoundly impacted on the new Scottish Executive. Research highlighting an obesity crisis facing young Scots has, together with the work of Scotland's Physical Activity Task Force and Physical Education Review Group, encouraged the education of all young Scots to be…

Scottish Schools Science Equipment Research Centre, Bulletin No. 61, February 1973.

ERIC Educational Resources Information Center

Scottish Schools Science Equipment Research Centre, Edinburgh.

This bulletin of the Scottish Schools Science Equipment Research Centre provides information to teachers regarding the use of newly produced equipment such as an economical soldering iron, nickel cadmium cell, and a desk calculator. Useful information is also included for teachers on the use of electric coils and bicarbonate indicators. A detailed…

Developing and Rewarding Excellent Teachers: The Scottish Chartered Teacher Scheme

ERIC Educational Resources Information Center

Ingvarson, Lawrence

2009-01-01

The Scottish Chartered Teacher Scheme was designed to recognise and reward teachers who attained high standards of practice. The scheme emerged in 2001 as part of an agreement between government, local employing authorities and teacher organisations. Policies such as the chartered teacher scheme aim to benefit students in two main ways: by…

Censorship Challenges to Books in Scottish Public Libraries

ERIC Educational Resources Information Center

Taylor, Kelly; McMenemy, David

2013-01-01

Censorship challenges to books in UK public libraries have received renewed attention recently. This study sought to establish the incidence of censorship challenges to books in Scottish public libraries in the years 2005-2009 and the actions taken in response to these challenges. It was found that eight local authorities in Scotland had received…

Social Justice and Provision for Children with Additional Support Needs in Scotland

ERIC Educational Resources Information Center

Riddell, Sheila; Weedon, Elisabet

2017-01-01

Since the re-establishment of the Scottish Parliament in 1999, successive administrations have reaffirmed their commitment to social justice. However, despite high-level equality policies, social-class inequality is a major feature of Scottish society, affecting all social policy domains, including education. In this article, we provide a brief…

Top-down proteomics for the analysis of proteolytic events - Methods, applications and perspectives.

PubMed

Tholey, Andreas; Becker, Alexander

2017-11-01

Mass spectrometry based proteomics is an indispensable tool for almost all research areas relevant for the understanding of proteolytic processing, ranging from the identification of substrates, products and cleavage sites up to the analysis of structural features influencing protease activity. The majority of methods for these studies are based on bottom-up proteomics performing analysis at peptide level. As this approach is characterized by a number of pitfalls, e.g. loss of molecular information, there is an ongoing effort to establish top-down proteomics, performing separation and MS analysis both at intact protein level. We briefly introduce major approaches of bottom-up proteomics used in the field of protease research and highlight the shortcomings of these methods. We then discuss the present state-of-the-art of top-down proteomics. Together with the discussion of known challenges we show the potential of this approach and present a number of successful applications of top-down proteomics in protease research. This article is part of a Special Issue entitled: Proteolysis as a Regulatory Event in Pathophysiology edited by Stefan Rose-John. Copyright © 2017 Elsevier B.V. All rights reserved.

Policy for home or hospice as the preferred place of death from cancer: Scottish Health and Ethnicity Linkage Study population cohort shows challenges across all ethnic groups in Scotland.

PubMed

Sharpe, Katharine H; Cezard, Genevieve; Bansal, Narinder; Bhopal, Raj S; Brewster, David H

2015-12-01

Place of cancer death varies ethnically and internationally. Palliative care reviews highlight limited ability to demonstrate equal access due to incomplete or unreliable ethnicity data. To establish place of cancer death by ethnicity and describe patient characteristics. We linked census, hospital episode and mortality data for 117 467 persons dying of cancer, 2001-2009. With White Scottish population as reference, prevalence ratios (PR), 95% CIs and p values of death in hospital, home or hospice adjusted for sex and age were calculated by ethnic group. White Scottish group and minority ethnic groups combined constituted 91% and 0.4% of cancer deaths, respectively. South Asian, Chinese and African Origin patients were youngest at death (66, 66 and 65.9 years). Compared with the Scottish White reference, the White Irish (1.15 (1.10 to 1.22), p<0.0001) and Other White British (1.07 (1.02 to 1.12), p=0.003) groups were more likely to die at home. Generally, affluent Scottish White patients were less likely to die in hospital and more likely to die at home or in a hospice regardless of socioeconomic indicator used. Cancer deaths occur most often in hospital (52.3%) for all ethnic groups. Regardless of the socioeconomic indicator used, more affluent Scottish White patients were less likely to die in hospital; existing socioeconomic indicators detected no clear trend for the non-White population. Regardless of ethnic group, significant work is required to achieve more people dying at home or the setting of their choice. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Expressing the human proteome for affinity proteomics: optimising expression of soluble protein domains and in vivo biotinylation.

PubMed

Keates, Tracy; Cooper, Christopher D O; Savitsky, Pavel; Allerston, Charles K; Phillips, Claire; Hammarström, Martin; Daga, Neha; Berridge, Georgina; Mahajan, Pravin; Burgess-Brown, Nicola A; Müller, Susanne; Gräslund, Susanne; Gileadi, Opher

2012-06-15

The generation of affinity reagents to large numbers of human proteins depends on the ability to express the target proteins as high-quality antigens. The Structural Genomics Consortium (SGC) focuses on the production and structure determination of human proteins. In a 7-year period, the SGC has deposited crystal structures of >800 human protein domains, and has additionally expressed and purified a similar number of protein domains that have not yet been crystallised. The targets include a diversity of protein domains, with an attempt to provide high coverage of protein families. The family approach provides an excellent basis for characterising the selectivity of affinity reagents. We present a summary of the approaches used to generate purified human proteins or protein domains, a test case demonstrating the ability to rapidly generate new proteins, and an optimisation study on the modification of >70 proteins by biotinylation in vivo. These results provide a unique synergy between large-scale structural projects and the recent efforts to produce a wide coverage of affinity reagents to the human proteome. Copyright © 2011 Elsevier B.V. All rights reserved.

Expressing the human proteome for affinity proteomics: optimising expression of soluble protein domains and in vivo biotinylation

PubMed Central

Keates, Tracy; Cooper, Christopher D.O.; Savitsky, Pavel; Allerston, Charles K.; Phillips, Claire; Hammarström, Martin; Daga, Neha; Berridge, Georgina; Mahajan, Pravin; Burgess-Brown, Nicola A.; Müller, Susanne; Gräslund, Susanne; Gileadi, Opher

2012-01-01

The generation of affinity reagents to large numbers of human proteins depends on the ability to express the target proteins as high-quality antigens. The Structural Genomics Consortium (SGC) focuses on the production and structure determination of human proteins. In a 7-year period, the SGC has deposited crystal structures of >800 human protein domains, and has additionally expressed and purified a similar number of protein domains that have not yet been crystallised. The targets include a diversity of protein domains, with an attempt to provide high coverage of protein families. The family approach provides an excellent basis for characterising the selectivity of affinity reagents. We present a summary of the approaches used to generate purified human proteins or protein domains, a test case demonstrating the ability to rapidly generate new proteins, and an optimisation study on the modification of >70 proteins by biotinylation in vivo. These results provide a unique synergy between large-scale structural projects and the recent efforts to produce a wide coverage of affinity reagents to the human proteome. PMID:22027370

The ribosomal subunit assembly line

PubMed Central

Dlakić, Mensur

2005-01-01

Recent proteomic studies in Saccharomyces cerevisiae have identified nearly 200 proteins, other than the structural ribosomal proteins, that participate in the assembly of ribosomal subunits and their transport from the nucleus. In a separate line of research, proteomic studies of mature plant ribosomes have revealed considerable variability in the protein composition of individual ribosomes. PMID:16207363

Personalized medicine beyond genomics: alternative futures in big data-proteomics, environtome and the social proteome.

PubMed

Özdemir, Vural; Dove, Edward S; Gürsoy, Ulvi K; Şardaş, Semra; Yıldırım, Arif; Yılmaz, Şenay Görücü; Ömer Barlas, I; Güngör, Kıvanç; Mete, Alper; Srivastava, Sanjeeva

2017-01-01

No field in science and medicine today remains untouched by Big Data, and psychiatry is no exception. Proteomics is a Big Data technology and a next generation biomarker, supporting novel system diagnostics and therapeutics in psychiatry. Proteomics technology is, in fact, much older than genomics and dates to the 1970s, well before the launch of the international Human Genome Project. While the genome has long been framed as the master or "elite" executive molecule in cell biology, the proteome by contrast is humble. Yet the proteome is critical for life-it ensures the daily functioning of cells and whole organisms. In short, proteins are the blue-collar workers of biology, the down-to-earth molecules that we cannot live without. Since 2010, proteomics has found renewed meaning and international attention with the launch of the Human Proteome Project and the growing interest in Big Data technologies such as proteomics. This article presents an interdisciplinary technology foresight analysis and conceptualizes the terms "environtome" and "social proteome". We define "environtome" as the entire complement of elements external to the human host, from microbiome, ambient temperature and weather conditions to government innovation policies, stock market dynamics, human values, political power and social norms that collectively shape the human host spatially and temporally. The "social proteome" is the subset of the environtome that influences the transition of proteomics technology to innovative applications in society. The social proteome encompasses, for example, new reimbursement schemes and business innovation models for proteomics diagnostics that depart from the "once-a-life-time" genotypic tests and the anticipated hype attendant to context and time sensitive proteomics tests. Building on the "nesting principle" for governance of complex systems as discussed by Elinor Ostrom, we propose here a 3-tiered organizational architecture for Big Data science such as proteomics. The proposed nested governance structure is comprised of (a) scientists, (b) ethicists, and (c) scholars in the nascent field of "ethics-of-ethics", and aims to cultivate a robust social proteome for personalized medicine. Ostrom often noted that such nested governance designs offer assurance that political power embedded in innovation processes is distributed evenly and is not concentrated disproportionately in a single overbearing stakeholder or person. We agree with this assessment and conclude by underscoring the synergistic value of social and biological proteomes to realize the full potentials of proteomics science for personalized medicine in psychiatry in the present era of Big Data.

Achievements and perspectives of top-down proteomics.

PubMed

Armirotti, Andrea; Damonte, Gianluca

2010-10-01

Over the last years, top-down (TD) MS has gained a remarkable space in proteomics, rapidly trespassing the limit between a promising approach and a solid, established technique. Several research groups worldwide have implemented TD analysis in their routine work on proteomics, deriving structural information on proteins with the level of accuracy that is impossible to achieve with classical bottom-up approaches. Complete maps of PTMs and assessment of single aminoacid polymorphisms are only a few of the results that can be obtained with this technique. Despite some existing technical and economical limitations, TD analysis is at present the most powerful instrument for MS-based proteomics and its implementation in routine workflow is a rapidly approaching turning point in proteomics. In this review article, the state-of-the-art of TD approach is described along with its major advantages and drawbacks and the most recent trends in TD analysis are discussed. References for all the covered topics are reported in the text, with the aim to support both newcomers and mass spectrometrists already introduced to TD proteomics.

The Scottish Council for Research in Education. Fifty-Sixth Annual Report, 1983-84.

ERIC Educational Resources Information Center

Scottish Council for Research in Education.

Brief reports are given of research projects worked on by staff members of the Scottish Council for Research in Education during 1983-84. Major projects included: (1) teaching strategies in the primary school; (2) second international (IEA) mathematics survey; (3) evaluation of the Craigroyston curriculum project; (4) further education for the…

Media Education in Scotland. Outline Proposals for a Curriculum.

ERIC Educational Resources Information Center

Robinson, T. K.; And Others

This document, prepared for the Scottish Council for Educational Technology and the Scottish Film Council, sets forth basic principles on which discussions of the future of media education in Scotland might be based. The nature and scope of media education are reviewed, and media education is portrayed as a means of helping children and adults to…

Who Gets to Play? Investigating Equity in Musical Instrument Instruction in Scottish Primary Schools

ERIC Educational Resources Information Center

Moscardini, Lio; Barron, David S.; Wilson, Alastair

2013-01-01

There is a widely held view that learning to play a musical instrument is a valuable experience for all children in terms of their personal growth and development. Although there is no statutory obligation for instrumental music provision in Scottish primary schools, there are well-established Instrumental Music Services in Local Education…

Ethics, Power, Internationalisation and the Postcolonial: A Foucauldian Discourse Analysis of Policy Documents in Two Scottish Universities

ERIC Educational Resources Information Center

Guion Akdag, Emma; Swanson, Dalene M.

2018-01-01

This paper provides a critical discussion of internationalisation in Higher Education (HE), and exemplifies a process of uncovering the investments in power and ideology through the partial analysis of four strategic internationalisation documents at two Scottish Higher Education institutions, as part of an ongoing international study into the…

Barriers to Higher Education Entry--A Scottish Rural Perspective

ERIC Educational Resources Information Center

Lasselle, Laurence

2016-01-01

This paper explores some of the unique issues in accessing Higher Education (HE) faced by pupils living in some Scottish rural communities in Argyll & Bute, Highland, Eilean Siar (Western Isles), Orkney Islands and Shetland Islands. Many of these communities are hard to reach and in some of the least deprived areas of Scotland. Despite this,…

Pulling Together in Adult Education. A History of the Scottish Institute of Adult and Continuing Education 1949-1989.

ERIC Educational Resources Information Center

Inglis, James; And Others

This document on the history of the Scottish Institute of Adult and Continuing Education (SIACE) includes seven papers as follows: "Preface" (E. Gerver); "The Beginnings 1949-1957" (J. Inglis); "The Institute under Tom Landsborough 1957-1971" (J. Inglis); "The Lean and Hungry Years 1971-1978" (J. Inglis);…

Collaborative Learning in the Scottish Curriculum for Excellence: The Challenges of Assessment and Potential of Multi-Touch Technology

ERIC Educational Resources Information Center

McKechan, Sandra; Ellis, Jennifer

2014-01-01

Scottish educational policy advocates the benefits of collaborative learning as a way of developing critical life skills, across the primary curriculum. In this paper, the rationale for collaborative learning, and specifically the Critical Skills (CS) approach, is considered along with an account of the perspectives of primary teachers…

Catholic Women Teachers and Scottish Education in the Nineteenth and Early Twentieth Centuries

ERIC Educational Resources Information Center

McDermid, Jane

2009-01-01

Catholics remained outside the Scottish educational system until 1918. The Church preferred mixed-sex infant schools and either single-sex schools or separate departments. In small towns and rural areas the schools were mixed-sex. Women were considered naturally best suited to teach infants and girls, but even in boys' schools, female assistants…

Changing Cognitions in Parents of Two-Year-Olds Attending Scottish Sure Start Centres

ERIC Educational Resources Information Center

Woolfson, Lisa Marks; Durkin, Kevin; King, Julia

2010-01-01

The study examined how preschool intervention programmes set up by three Scottish local authorities changed parents' cognitions. Quantitative parent outcomes were measured using Parenting Daily Hassles Scales (N = 88). A matched comparison group of parents (N = 55) recruited from the same areas of disadvantage but whose children did not attend the…

The Scottish Council for Research in Education. Forty-Fourth Annual Report, 1971-72.

ERIC Educational Resources Information Center

Scottish Council for Research in Education.

This booklet contains the annual report for 1971-72 of the Scottish Council for Research in Education. The first section lists the officers, members, principle officials, and staff responsible for special projects. The second section presents reports from the various committees of the council, stressing the reconstruction of the council's…

Incorporating Scottish Highland Games and Activities into Your Physical Education Classes

ERIC Educational Resources Information Center

Prewitt, Steven L.; Hannon, James C.; Brusseau, Timothy

2015-01-01

The purpose of this article is to introduce a potentially new and exciting group of activities that can be taught in physical education. Activities based on Scottish Highland Games can be an interesting way to incorporate history and literature into the curriculum, as well as introduce students to a variety of unique physical activities. This…

Scottish Premier League Reading Stars Evaluation Report

ERIC Educational Resources Information Center

National Literacy Trust, 2009

2009-01-01

Scottish Premier League (SPL) Reading Stars uses the motivational power of football to attract families who need support with literacy into a positive and friendly learning environment. It ran for the first time between March and August 2009 and attracted 225 children and 190 adults to take part in a series of inspirational learning sessions in 23…

Are "Communications Frameworks" More Successful? Policy Learning from the Scottish Credit and Qualifications Framework

ERIC Educational Resources Information Center

Raffe, David

2011-01-01

The Scottish Credit and Qualifications Framework (SCQF) was formally launched in 2001. It is a comprehensive credit-based National Qualifications Framework (NQF) with twelve levels, intended to accommodate all qualifications and assessed learning in Scotland. It aims to support access to learning and to make the education and training system more…

Revolution, Evolution or a Trojan Horse? Piloting Assessment for Learning in Some Scottish Primary Schools

ERIC Educational Resources Information Center

Kirton, Alison; Hallam, Susan; Peffers, Jack; Robertson, Pamela; Stobart, Gordon

2007-01-01

This article analyses some of the findings of an evaluation of Project One of the "Assessment is for Learning" Development Programme in 16 Scottish primary schools and two junior high schools in which teachers developed formative assessment strategies aimed at improving teaching and learning. Drawing on data from pupils, teachers and…

A Long Path to Divergence: English and Scottish Policies on Tuition Fees

ERIC Educational Resources Information Center

Bratberg, Oivind

2011-01-01

This article addresses the diverging policies of England and Scotland since 1999 on the issue of tuition fees. While the UK Parliament has introduced (and henceforth enhanced the level of) tuition fees for students at English universities, the Scottish Parliament has refuted fees in two successive stages. In this article I trace the political…

A 'Scottish Poor Law of Lunacy'? Poor Law, Lunacy Law and Scotland's parochial asylums.

PubMed

Farquharson, Lauren

2017-03-01

Scotland's parochial asylums are unfamiliar institutional spaces. Representing the concrete manifestation of the collision between two spheres of legislation, the Poor Law and the Lunacy Law, six such asylums were constructed in the latter half of the nineteenth century. These sites expressed the enduring mandate of the Scottish Poor Law 1845 over the domain of 'madness'. They were institutions whose very existence was fashioned at the directive of the local arm of the Poor Law, the parochial board, and they constituted a continuing 'Scottish Poor Law of Lunacy'. Their origins and operation significantly subverted the intentions and objectives of the Lunacy Act 1857, the aim of which had been to institute a public district asylum network with nationwide coverage.

Enriching the annotation of Mycobacterium tuberculosis H37Rv proteome using remote homology detection approaches: insights into structure and function.

PubMed

Ramakrishnan, Gayatri; Ochoa-Montaño, Bernardo; Raghavender, Upadhyayula S; Mudgal, Richa; Joshi, Adwait G; Chandra, Nagasuma R; Sowdhamini, Ramanathan; Blundell, Tom L; Srinivasan, Narayanaswamy

2015-01-01

The availability of the genome sequence of Mycobacterium tuberculosis H37Rv has encouraged determination of large numbers of protein structures and detailed definition of the biological information encoded therein; yet, the functions of many proteins in M. tuberculosis remain unknown. The emergence of multidrug resistant strains makes it a priority to exploit recent advances in homology recognition and structure prediction to re-analyse its gene products. Here we report the structural and functional characterization of gene products encoded in the M. tuberculosis genome, with the help of sensitive profile-based remote homology search and fold recognition algorithms resulting in an enhanced annotation of the proteome where 95% of the M. tuberculosis proteins were identified wholly or partly with information on structure or function. New information includes association of 244 proteins with 205 domain families and a separate set of new association of folds to 64 proteins. Extending structural information across uncharacterized protein families represented in the M. tuberculosis proteome, by determining superfamily relationships between families of known and unknown structures, has contributed to an enhancement in the knowledge of structural content. In retrospect, such superfamily relationships have facilitated recognition of probable structure and/or function for several uncharacterized protein families, eventually aiding recognition of probable functions for homologous proteins corresponding to such families. Gene products unique to mycobacteria for which no functions could be identified are 183. Of these 18 were determined to be M. tuberculosis specific. Such pathogen-specific proteins are speculated to harbour virulence factors required for pathogenesis. A re-annotated proteome of M. tuberculosis, with greater completeness of annotated proteins and domain assigned regions, provides a valuable basis for experimental endeavours designed to obtain a better understanding of pathogenesis and to accelerate the process of drug target discovery. Copyright © 2014 Elsevier Ltd. All rights reserved.

Joining Forces: Integrating Proteomics and Cross-linking with the Mass Spectrometry of Intact Complexes*

PubMed Central

Stengel, Florian; Aebersold, Ruedi; Robinson, Carol V.

2012-01-01

Protein assemblies are critical for cellular function and understanding their physical organization is the key aim of structural biology. However, applying conventional structural biology approaches is challenging for transient, dynamic, or polydisperse assemblies. There is therefore a growing demand for hybrid technologies that are able to complement classical structural biology methods and thereby broaden our arsenal for the study of these important complexes. Exciting new developments in the field of mass spectrometry and proteomics have added a new dimension to the study of protein-protein interactions and protein complex architecture. In this review, we focus on how complementary mass spectrometry-based techniques can greatly facilitate structural understanding of protein assemblies. PMID:22180098

compomics-utilities: an open-source Java library for computational proteomics.

PubMed

Barsnes, Harald; Vaudel, Marc; Colaert, Niklaas; Helsens, Kenny; Sickmann, Albert; Berven, Frode S; Martens, Lennart

2011-03-08

The growing interest in the field of proteomics has increased the demand for software tools and applications that process and analyze the resulting data. And even though the purpose of these tools can vary significantly, they usually share a basic set of features, including the handling of protein and peptide sequences, the visualization of (and interaction with) spectra and chromatograms, and the parsing of results from various proteomics search engines. Developers typically spend considerable time and effort implementing these support structures, which detracts from working on the novel aspects of their tool. In order to simplify the development of proteomics tools, we have implemented an open-source support library for computational proteomics, called compomics-utilities. The library contains a broad set of features required for reading, parsing, and analyzing proteomics data. compomics-utilities is already used by a long list of existing software, ensuring library stability and continued support and development. As a user-friendly, well-documented and open-source library, compomics-utilities greatly simplifies the implementation of the basic features needed in most proteomics tools. Implemented in 100% Java, compomics-utilities is fully portable across platforms and architectures. Our library thus allows the developers to focus on the novel aspects of their tools, rather than on the basic functions, which can contribute substantially to faster development, and better tools for proteomics.

Ova fecundity in Scottish Atlantic salmon Salmo salar: predictions, selective forces and causal mechanisms.

PubMed

Bacon, P J; MacLean, J C; Malcolm, I A; Gurney, W S C

2012-08-01

Ova fecundities of Scottish Atlantic salmon Salmo salar, predicted from log(10) regression of ova numbers and female fork length (L(F)), differed widely between upland and lowland stocks within the same river, whereas sea-age, river and year factors had insignificant effects on fecundity once L(F) was accounted for. For upland fish, the relationship between log(10)L(F) and log(10) ova mass (M(O)) was stable between two datasets collected 40 years apart. Although upland and lowland females both produced comparable log(10)M(O) (log(10)L(F))(-1), lowland females partitioned this into 45% more, but smaller ova, whereas upland females produced fewer, but larger, eggs. The possible causes and implications of this are discussed for evolutionary perspectives (lifetime production), population structure (local tributary v. large catchments; environmental effects), population dynamics and stability (density-dependent control mechanisms) and fisheries management (stock-recruitment; short and long-term stock sustainability). © 2012 Marine Scotland. Journal of Fish Biology © 2012 The Fisheries Society of the British Isles.

Becoming independent: political participation and youth transitions in the Scottish referendum.

PubMed

Breeze, Maddie; Gorringe, Hugo; Jamieson, Lynn; Rosie, Michael

2017-12-01

Sociological debates on youth engagement with electoral politics play out against a backdrop of supposed 'decline' in civic participation (e.g. Putnam , Norris, ), in turn contextualized by theories of individualization in 'late' or 'reflexive' modernity (Beck, Giddens). However, the enfranchisement of 16 and 17 year olds in the 2014 Scottish Independence Referendum catalysed remarkably high levels of voter turnout among this youngest group, and was accompanied by apparently ongoing political engagement. We explored this engagement among a strategic sample of young 'Yes' voters, in the immediate aftermath of this exceptional political event. Analysis of qualitative interview data generated an unanticipated finding; that interviewees narrated their political engagement biographically, articulated their referendum participation reflexively, and located their new political ideas, allegiances and actions in the context of their own transitions to 'independent' adulthood. This inspired us to rethink young people's political engagement in relation to youth transitions. Doing so enables a synthesis of divergent strands in the sociology of youth, and offers new insights into the combinations of 'personal' agentic and 'political' structural factors involved in young people's politicization. © London School of Economics and Political Science 2017.

Health governance--its introduction in Lanarkshire Health Board.

PubMed

Wrench, J G; Moir, D C

2002-01-01

To describe an approach to implementing the principles of clinical governance in a Health Board setting. Using guidance from the Scottish Executive and The Faculty of Public Health Medicine to set up a health governance structure at Health Board level. Auditing current work to identify areas that required to be progressed. Lanarkshire Health Board. A Health Governance Committee and a Health Governance Advisory Group, to support the work of the main committee, were set up at Board level. The Scottish Executive Governance Monitoring Template has been adapted to cover the main public health functions. Topics considered in the first year include qualifications, registration and CPD activity of Consultants in Public Health Medicine, audit of public health advice on gastro-intestinal illness, audit of DPH Annual Report and audit of items of business on Health Board agenda. The model developed in Lanarkshire has a Health Governance Advisory Group which works in support of the main Health Governance Committee. This model works well in practice with much of the routine work being done by the Advisory Group. This has streamlined the work of the Health Governance Committee and facilitated its introduction.

Previously unknown apicomplexan species infecting Iceland scallop, Chlamys islandica (Müller, 1776), queen scallop, Aequipecten opercularis L., and king scallop, Pecten maximus L.

PubMed

Kristmundsson, Árni; Helgason, Sigurður; Bambir, Slavko Helgi; Eydal, Matthías; Freeman, Mark A

2011-11-01

Examination of three scallop species from three separate locations: Iceland scallop from Icelandic waters, king scallop from Scottish waters and queen scallop from Faroese and Scottish waters, revealed infections of a previously unknown apicomplexan parasite in all three scallop species. Developmental forms observed in the shells appeared to include both sexual and asexual stages of the parasite, i.e. merogony, gametogony and sporogony, which suggests a monoxenous life cycle. Meronts, gamonts, zygotes and mature oocysts were solely found in the muscular tissue. Zoites, which could be sporozoites and/or merozoites, were observed in great numbers, most frequently in muscles, both intracellular and free in the extracellular space. Zoites were also common inside haemocytes. Examination of the ultrastructure showed that the zoites contained all the major structures characterizing apicomplexans. This apicomplexan parasite is morphologically different from other apicomplexan species previously described from bivalves. Presently, its systematic position within the phylum Apicomplexa cannot be ascertained. Copyright © 2011 Elsevier Inc. All rights reserved.

Global Analysis Reveals the Complexity of the Human Glomerular Extracellular Matrix

PubMed Central

Byron, Adam; Humphries, Jonathan D.; Randles, Michael J.; Carisey, Alex; Murphy, Stephanie; Knight, David; Brenchley, Paul E.; Zent, Roy; Humphries, Martin J.

2014-01-01

The glomerulus contains unique cellular and extracellular matrix (ECM) components, which are required for intact barrier function. Studies of the cellular components have helped to build understanding of glomerular disease; however, the full composition and regulation of glomerular ECM remains poorly understood. We used mass spectrometry-based proteomics of enriched ECM extracts for a global analysis of human glomerular ECM in vivo and identified a tissue-specific proteome of 144 structural and regulatory ECM proteins. This catalog includes all previously identified glomerular components plus many new and abundant components. Relative protein quantification showed a dominance of collagen IV, collagen I, and laminin isoforms in the glomerular ECM together with abundant collagen VI and TINAGL1. Protein network analysis enabled the creation of a glomerular ECM interactome, which revealed a core of highly connected structural components. More than one half of the glomerular ECM proteome was validated using colocalization studies and data from the Human Protein Atlas. This study yields the greatest number of ECM proteins relative to previous investigations of whole glomerular extracts, highlighting the importance of sample enrichment. It also shows that the composition of glomerular ECM is far more complex than previously appreciated and suggests that many more ECM components may contribute to glomerular development and disease processes. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the dataset identifier PXD000456. PMID:24436468

Clinical features of progressive vacuolar hepatopathy in Scottish Terriers with and without hepatocellular carcinoma: 114 cases (1980-2013).

PubMed

Cortright, Catherine C; Center, Sharon A; Randolph, John F; McDonough, Sean P; Fecteau, Kellie A; Warner, Karen L; Chiapella, Ann M; Pierce, Rhonda L; Graham, A Heather; Wall, Linda J; Heidgerd, John H; Degen, Melisa A; Lucia, Patricia A; Erb, Hollis N

2014-10-01

To characterize signalment, clinical features, clinicopathologic variables, hepatic ultrasonographic characteristics, endocrinologic profiles, treatment response, and age at death of Scottish Terriers with progressive vacuolar hepatopathy (VH) with or without hepatocellular carcinoma (HCC). Retrospective case series. 114 Scottish Terriers with progressive VH. Electronic databases from 1980 to 2013 were searched for adult (age > 1 year) Scottish Terriers with histopathologic diagnoses of diffuse glycogen-like VH. Available sections of liver specimens were histologically reevaluated to confirm diffuse VH with or without HCC; 8 dogs with HCC only had neoplastic tissue available. Physical examination, clinicopathologic, treatment, and survival data were obtained. 39 of 114 (34%) dogs with VH had HCC detected at surgery or necropsy or by abdominal ultrasonography. Histologic findings indicated that HCC was seemingly preceded by dysplastic hepatocellular foci. No significant differences were found in clinicopathologic variables or age at death between VH-affected dogs with or without HCC. Fifteen of 26 (58%) dogs with high hepatic copper concentrations had histologic features consistent with copper-associated hepatopathy. Although signs consistent with hyperadrenocorticism were observed in 40% (46/114) of dogs, definitive diagnosis was inconsistently confirmed. Assessment of adrenal sex hormone concentrations before and after ACTH administration identified high progesterone and androstenedione concentrations in 88% (22/25) and 80% (20/25) of tested dogs, respectively. Results suggested that VH in Scottish Terriers may be linked to adrenal steroidogenesis and a predisposition to HCC. In dogs with VH, frequent serum biochemical analysis and ultrasonographic surveillance for early tumor detection are recommended.

Proteome Comparisons between Hemolymph of Two Honeybee Strains (Apis mellifera ligustica) Reveal Divergent Molecular Basis in Driving Hemolymph Function and High Royal Jelly Secretion.

PubMed

Ararso, Zewdu; Ma, Chuan; Qi, Yuping; Feng, Mao; Han, Bin; Hu, Han; Meng, Lifeng; Li, Jianke

2018-01-05

Hemolymph is vital for the immunity of honeybees and offers a way to investigate their physiological status. To gain novel insight into the functionality and molecular details of the hemolymph in driving increased Royal Jelly (RJ) production, we characterized and compared hemolymph proteomes across the larval and adult ages of Italian bees (ITbs) and Royal Jelly bees (RJbs), a stock selected from ITbs for increasing RJ output. Unprecedented in-depth proteome was attained with the identification of 3394 hemolymph proteins in both bee lines. The changes in proteome support the general function of hemolymph to drive development and immunity across different ages. However, age-specific proteome settings have adapted to prime the distinct physiology for larvae and adult bees. In larvae, the proteome is thought to drive temporal immunity, rapid organogenesis, and reorganization of larval structures. In adults, the proteome plays key roles in prompting tissue development and immune defense in newly emerged bees, in gland maturity in nurse bees, and in carbohydrate energy production in forager bees. Between larval and adult samples of the same age, RJbs and ITbs have tailored distinct hemolymph proteome programs to drive their physiology. In particular, in day 4 larvae and nurse bees, a large number of highly abundant proteins are enriched in protein synthesis and energy metabolism in RJbs. This implies that they have adapted their proteome to initiate different developmental trajectories and high RJ secretion in response to selection for enhanced RJ production. Our hitherto unexplored in-depth proteome coverage provides novel insight into molecular details that drive hemolymph function and high RJ production by RJbs.

Bacterial membrane proteomics.

PubMed

Poetsch, Ansgar; Wolters, Dirk

2008-10-01

About one quarter to one third of all bacterial genes encode proteins of the inner or outer bacterial membrane. These proteins perform essential physiological functions, such as the import or export of metabolites, the homeostasis of metal ions, the extrusion of toxic substances or antibiotics, and the generation or conversion of energy. The last years have witnessed completion of a plethora of whole-genome sequences of bacteria important for biotechnology or medicine, which is the foundation for proteome and other functional genome analyses. In this review, we discuss the challenges in membrane proteome analysis, starting from sample preparation and leading to MS-data analysis and quantification. The current state of available proteomics technologies as well as their advantages and disadvantages will be described with a focus on shotgun proteomics. Then, we will briefly introduce the most abundant proteins and protein families present in bacterial membranes before bacterial membrane proteomics studies of the last years will be presented. It will be shown how these works enlarged our knowledge about the physiological adaptations that take place in bacteria during fine chemical production, bioremediation, protein overexpression, and during infections. Furthermore, several examples from literature demonstrate the suitability of membrane proteomics for the identification of antigens and different pathogenic strains, as well as the elucidation of membrane protein structure and function.

The Scottish Council for Research in Education. Fifty-Seventh Annual Report 1984-85.

ERIC Educational Resources Information Center

Scottish Council for Research in Education.

This 1984-85 annual report from the Scottish Council for Research in Education (SCRE) contains lists of officers, members, principal officials and staff; the chairman's report for 1984-85; a summary of projects in tabular form and a series of brief reports on projects; a note on overseas counsultancies; a list of SCRE publications; a note on…

Scottish and Slovak University Student Discussions about Stigmatized Persons: A Challenge for Education--Moving towards Democracy and Inclusion

ERIC Educational Resources Information Center

Plichtová, Jana

2013-01-01

The paper compares discussions in 12 groups of university students (6 Slovak and 6 Scottish) equal in sex and age. The participants discussed the same problem--how to control the spread of HIV/AIDS and respect medical confidentiality (MC). Systematic comparisons revealed striking differences between the two national groups. The Scottish…

The Treasure House of a Nation? Literary Heritage, Curriculum and Devolution in Scotland and England in the Twenty-First Century

ERIC Educational Resources Information Center

Elliott, Victoria

2014-01-01

In January 2012, Scotland's First Minister Alex Salmond announced a radical measure that would see every Scottish school student study a Scottish text from a prescribed list. In 2010, Michael Gove announced that "Our literature is the best in the world" and that every pupil should study particular authors. The "cultural…

Position Paper: Should the Scottish National Party Support Scotland to Legalize, Decriminalize, or Prohibit Cannabis?

ERIC Educational Resources Information Center

Jhaveri, Sujata

2005-01-01

The UK has the highest rate of cannabis use among young people worldwide. Dr. Alan Leshner, Director of the National Institute of Drug Abuse reports, "Every year more than 100,000 people, most of them adolescents, seek treatment for their inability to control their marijuana use." According to the Scottish Drug Misuse Statistics in…

Getting the best value from refurb projects.

PubMed

Dimitrijevic, Branka

2013-04-01

Professor Branka Dimitrijevic, director of CIC Start Online, a project funded by the Scottish Government and European Regional Development Fund combining the resources of seven Scottish universities that aims to embed sustainable building design and refurbishment into practice, reports on a conference jointly staged in Glasgow recently by the organisation and Health Facilities Scotland that considered this topical issue in some depth.

The Decline of Gaelic in Northern Scotland, 1698-1901. Discussion Papers in Geolinguistics 7.

ERIC Educational Resources Information Center

Withers, Charles W. J.

This study examines the changing patterns of usage of Scottish Gaelic and English in the northern Scottish counties of Sutherland and Caithness during the period 1698-1901. The study explores the way these patterns resulted from processes found in different social situations. It is concluded that although the shift from Gaelic to English was not…

The Quality of Perceived Parenting Experienced by a Group of Scottish Incarcerated Young Offenders and Its Relation to Psychological Distress.

ERIC Educational Resources Information Center

Biggam, Fiona H.; Power, Kevin G.

1998-01-01

Utilizes the Parental Bonding Instrument with a group of 125 incarcerated Scottish young offenders 16-21 years old. Examines the response profiles of young participants and compares the results to normative data and demographics relating to family and penal experiences. Also investigates relationships between parenting style and levels of…

Indisciplines of Inquiry: The Scottish "Children's Story", Documentary Film and the Construction of the Viewer

ERIC Educational Resources Information Center

Cabeleira, Helena; Martins, Catarina; Lawn, Martin

2011-01-01

The starting point for this article is a film about Scottish education, "Children's Story". "Children's Story" was one of a group of seven documentaries made for the 1938 British Empire Exhibition in Glasgow, under the supervision of John Grierson. The film was an official entry into the Exhibition and is a formal display of…

Problematising "Education" and "Training" in the Scottish Sport and Fitness, Play and Outdoor Sectors

ERIC Educational Resources Information Center

Foley, M.; Frew, M.; McGillivray, D.; McIntosh, A.; McPherson, G.

2004-01-01

Sets out the issues peculiar to the Scottish workforce in sport and fitness, play and the outdoor sectors. Provides an exploration of the development of vocational education in the form of sector skills training for these sectors in opposition to that formal education provided at further and higher education level. Draws on empirical research…

Middle Managers' Experience of Policy Implementation and Mediation in the Context of the Scottish Quality Enhancement Framework

ERIC Educational Resources Information Center

Saunders, Murray; Sin, Cristina

2015-01-01

This paper analyses how middle managers perform and experience their role in enacting policy in Scottish higher education institutions. The policy focus is the quality enhancement framework (QEF) for learning and teaching in higher education, which was launched in 2003. The data-set was collected between 2008 and 2010, during the evaluation of the…

Expectations and Challenges: The Implementation of Mobile Devices in a Scottish Primary School

ERIC Educational Resources Information Center

Cornelius, Sarah; Shanks, Rachel

2017-01-01

This article provides a case study of the implementation of iPod Touches on a one-to-one basis in a Scottish primary school. It focuses on teachers' expectations for the project and the realisation (or otherwise) of these expectations. Findings suggest that the iPods offered opportunities for resource provision, interactive learning and extension…

Using Thematic Units To Promote Literacy in a Scottish Classroom.

ERIC Educational Resources Information Center

Erwin, Barbara; And Others

Using a literature-based thematic unit to teach language arts in concert with science, social studies, mathematics, and art, a Scottish teacher instilled in her 6- and 7-year-old pupils an understanding of their own lives, a love for language, and a feeling of satisfaction and pride in their accomplishments. The teacher developed a topic based on…

Brief Report: Self-Harm Is Associated with Immature Defense Mechanisms but Not Substance Use in a Nonclinical Scottish Adolescent Sample

ERIC Educational Resources Information Center

Brody, Stuart; Carson, Carron Maryjane

2012-01-01

It has been unclear whether adolescent deliberate self-harm (DSH) is more associated with substance use or with characterological impairments. Multivariate determination of (N = 114 Scottish adolescents) ever engaging in DSH (Youth Risk Behavior Survey) from alcohol use, other substance use, and immature defense mechanism use (Defense Style…

Youth Employment, Psychosocial Health and the Importance of Person/Environment Fit: A Case Study of Two Scottish Rural Towns.

ERIC Educational Resources Information Center

Pavis, Stephen; Platt, Stephen; Hubbard, Gill

2002-01-01

Reports on the employment experiences of young people from two small rural Scottish towns. The majority of available employment was repetitive, and involved poor working conditions and limited opportunity for skill development or promotion. Most respondents recognized that in the longer term such work was detrimental to their quality of life and…

Social Relationships and Health: The Meaning of Social "Connectedess" and How It Relates to Health Concerns for Rural Scottish Adolescents.

ERIC Educational Resources Information Center

Hendry, Leo B.; Reid, Marylou

2000-01-01

Discusses social belonging as both a health-related goal and an antidote for emotional crises. Examines how social connectedess represents both a content and process variable in Northern Scottish young people's discussion of their health concerns. Analyses reveal both the potency of all these concerns and participants' belief that skills acquired…

Finding the Way: Improving Access to the Collections of the Royal Scottish Geographical Society

ERIC Educational Resources Information Center

Fenton, Candida

2007-01-01

Purpose: The purpose of this paper is to describe the Images for All digitisation project at the Royal Scottish Geographical Society, and lessons learned from it. Design/methodology/approach: This paper describes the background to the project and collections held. It focuses on the development of the project web site, the digitisation of 100…

Science Topics for Third and Fourth Year Non-S.C.E. Courses.

ERIC Educational Resources Information Center

Scottish Education Dept., Edinburgh.

This publication contains details of 18 science topics based upon the general science objectives stated by the Working Party on Secondary School Science for pupils in the third and fourth years of Scottish secondary schools who do not intend to take courses leading to the Scottish Certificate of Education examinations (see SE 015 432). The topics…

Educational Commitments in the 2016 Election to the Scottish Parliament: An Analysis of Party Manifestos

ERIC Educational Resources Information Center

Humes, Walter

2017-01-01

This paper examines the 2016 manifestos of the main political parties seeking election to the Scottish Parliament, with particular reference to their educational commitments on issues of equality and inclusion. The policy context is described and related to academic accounts of the policy-making process. Use is made of discourse analysis as a…

What motivates dentists to work in prisons? A qualitative exploration.

PubMed

Smith, P A; Themessl-Huber, M; Akbar, T; Richards, D; Freeman, R

2011-08-26

To explore what motivates dentists to work in prisons using Vroom's theoretical model of motivation as an explanatory framework. In-depth interviews were conducted with ten of the 15 dentists working in Scottish prisons. The focus was to explore their motivations to work in Scottish prisons. The data were analysed using a thematic framework based on the three motivational dimensions of expectancy, instrumentality and valence. The dentists had the skills to help improve their prisoner-patients' oral health but their efforts were often hindered by institutional rationing and the requirement to fit in with prison routines and procedures (expectancy). Despite these institutional difficulties the dentists experienced work rewards associated with the improvement in the prisoners' oral health (instrumentality). Finally, the dentists experienced a feeling of personal worth and a sense of commitment to providing care to Scottish prisoners (valence). The dentists' motivation to work in Scottish prisons may be explained by Vroom's Expectancy Theory. The dentists' motivation is characterised by their beliefs that their work will improve clinical outcomes which will be rewarded by the satisfaction experienced when they overcome environmental obstacles and provide oral health care for their prisoner-patients.

CSF proteomic fingerprints for HIV-associated cognitive impairment.

PubMed

Laspiur, Juliana Pérez; Anderson, Eric R; Ciborowski, Pawel; Wojna, Valerie; Rozek, Wojciech; Duan, Fenghai; Mayo, Raul; Rodríguez, Elaine; Plaud-Valentín, Marinés; Rodríguez-Orengo, José; Gendelman, Howard E; Meléndez, Loyda M

2007-12-01

Cognitive impairment remains a major complication of advanced human immunodeficiency virus (HIV) infection despite the widespread use of anti-retroviral therapy. Diagnosis is made by exclusion making biomarkers of great potential use. Thus, we used an integrated proteomics platform to assess cerebrospinal fluid protein profiles from 50 HIV-1 seropositive Hispanic women. Nine of 38 proteins identified were unique in those patients with cognitive impairment (CI). These proteins were linked to cell signaling, structural function, and antioxidant activities. This work highlights, in a preliminary manner, the utility of proteomic profiling for biomarker discovery for HIV-1 associated cognitive dysfunction.

CSF proteomic fingerprints for HIV- associated cognitive impairment

PubMed Central

Laspiur, Juliana Pérez; Anderson, Eric R.; Ciborowski, Pawel; Wojna, Valerie; Rozek, Wojciech; Duan, Fenghai; Mayo, Raul; Rodríguez, Elaine; Plaud-Valentín, Marinés; Rodríguez-Orengo, José; Gendelman, Howard E.; Meléndez, Loyda M.

2008-01-01

Cognitive impairment remains a major complication of advanced human immunodeficiency virus (HIV) infection despite the wide spread use of anti-retroviral therapy. Diagnosis is made by exclusion making biomarkers of great potential use. Thus, we used an integrated proteomics platform to assess cerebrospinal fluid protein profiles from 50 HIV-1 seropositive Hispanic women. Nine of 38 proteins identified were unique in those patients with cognitive impairment. These proteins were linked to cell signaling, structural function, and antioxidant activities. This work highlights, in a preliminary manner, the utility of proteomic profiling for biomarker discovery for HIV-1 associated cognitive dysfunction. PMID:17950469

Sequence/structural analysis of xylem proteome emphasizes pathogenesis-related proteins, chitinases and β-1, 3-glucanases as key players in grapevine defense against Xylella fastidiosa.

PubMed

Chakraborty, Sandeep; Nascimento, Rafael; Zaini, Paulo A; Gouran, Hossein; Rao, Basuthkar J; Goulart, Luiz R; Dandekar, Abhaya M

2016-01-01

Background. Xylella fastidiosa, the causative agent of various plant diseases including Pierce's disease in the US, and Citrus Variegated Chlorosis in Brazil, remains a continual source of concern and economic losses, especially since almost all commercial varieties are sensitive to this Gammaproteobacteria. Differential expression of proteins in infected tissue is an established methodology to identify key elements involved in plant defense pathways. Methods. In the current work, we developed a methodology named CHURNER that emphasizes relevant protein functions from proteomic data, based on identification of proteins with similar structures that do not necessarily have sequence homology. Such clustering emphasizes protein functions which have multiple copies that are up/down-regulated, and highlights similar proteins which are differentially regulated. As a working example we present proteomic data enumerating differentially expressed proteins in xylem sap from grapevines that were infected with X. fastidiosa. Results. Analysis of this data by CHURNER highlighted pathogenesis related PR-1 proteins, reinforcing this as the foremost protein function in xylem sap involved in the grapevine defense response to X. fastidiosa. β-1, 3-glucanase, which has both anti-microbial and anti-fungal activities, is also up-regulated. Simultaneously, chitinases are found to be both up and down-regulated by CHURNER, and thus the net gain of this protein function loses its significance in the defense response. Discussion. We demonstrate how structural data can be incorporated in the pipeline of proteomic data analysis prior to making inferences on the importance of individual proteins to plant defense mechanisms. We expect CHURNER to be applicable to any proteomic data set.

Single Amino Acid Repeats in the Proteome World: Structural, Functional, and Evolutionary Insights

PubMed Central

Kumar, Amitha Sampath; Sowpati, Divya Tej; Mishra, Rakesh K.

2016-01-01

Microsatellites or simple sequence repeats (SSR) are abundant, highly diverse stretches of short DNA repeats present in all genomes. Tandem mono/tri/hexanucleotide repeats in the coding regions contribute to single amino acids repeats (SAARs) in the proteome. While SSRs in the coding region always result in amino acid repeats, a majority of SAARs arise due to a combination of various codons representing the same amino acid and not as a consequence of SSR events. Certain amino acids are abundant in repeat regions indicating a positive selection pressure behind the accumulation of SAARs. By analysing 22 proteomes including the human proteome, we explored the functional and structural relationship of amino acid repeats in an evolutionary context. Only ~15% of repeats are present in any known functional domain, while ~74% of repeats are present in the disordered regions, suggesting that SAARs add to the functionality of proteins by providing flexibility, stability and act as linker elements between domains. Comparison of SAAR containing proteins across species reveals that while shorter repeats are conserved among orthologs, proteins with longer repeats, >15 amino acids, are unique to the respective organism. Lysine repeats are well conserved among orthologs with respect to their length and number of occurrences in a protein. Other amino acids such as glutamic acid, proline, serine and alanine repeats are generally conserved among the orthologs with varying repeat lengths. These findings suggest that SAARs have accumulated in the proteome under positive selection pressure and that they provide flexibility for optimal folding of functional/structural domains of proteins. The insights gained from our observations can help in effective designing and engineering of proteins with novel features. PMID:27893794

Accelerating the design of biomimetic materials by integrating RNA-seq with proteomics and materials science.

PubMed

Guerette, Paul A; Hoon, Shawn; Seow, Yiqi; Raida, Manfred; Masic, Admir; Wong, Fong T; Ho, Vincent H B; Kong, Kiat Whye; Demirel, Melik C; Pena-Francesch, Abdon; Amini, Shahrouz; Tay, Gavin Z; Ding, Dawei; Miserez, Ali

2013-10-01

Efforts to engineer new materials inspired by biological structures are hampered by the lack of genomic data from many model organisms studied in biomimetic research. Here we show that biomimetic engineering can be accelerated by integrating high-throughput RNA-seq with proteomics and advanced materials characterization. This approach can be applied to a broad range of systems, as we illustrate by investigating diverse high-performance biological materials involved in embryo protection, adhesion and predation. In one example, we rapidly engineer recombinant squid sucker ring teeth proteins into a range of structural and functional materials, including nanopatterned surfaces and photo-cross-linked films that exceed the mechanical properties of most natural and synthetic polymers. Integrating RNA-seq with proteomics and materials science facilitates the molecular characterization of natural materials and the effective translation of their molecular designs into a wide range of bio-inspired materials.

Improved Recovery and Identification of Membrane Proteins from Rat Hepatic Cells using a Centrifugal Proteomic Reactor*

PubMed Central

Zhou, Hu; Wang, Fangjun; Wang, Yuwei; Ning, Zhibin; Hou, Weimin; Wright, Theodore G.; Sundaram, Meenakshi; Zhong, Shumei; Yao, Zemin; Figeys, Daniel

2011-01-01

Despite their importance in many biological processes, membrane proteins are underrepresented in proteomic analysis because of their poor solubility (hydrophobicity) and often low abundance. We describe a novel approach for the identification of plasma membrane proteins and intracellular microsomal proteins that combines membrane fractionation, a centrifugal proteomic reactor for streamlined protein extraction, protein digestion and fractionation by centrifugation, and high performance liquid chromatography-electrospray ionization-tandem MS. The performance of this approach was illustrated for the study of the proteome of ER and Golgi microsomal membranes in rat hepatic cells. The centrifugal proteomic reactor identified 945 plasma membrane proteins and 955 microsomal membrane proteins, of which 63 and 47% were predicted as bona fide membrane proteins, respectively. Among these proteins, >800 proteins were undetectable by the conventional in-gel digestion approach. The majority of the membrane proteins only identified by the centrifugal proteomic reactor were proteins with ≥2 transmembrane segments or proteins with high molecular mass (e.g. >150 kDa) and hydrophobicity. The improved proteomic reactor allowed the detection of a group of endocytic and/or signaling receptor proteins on the plasma membrane, as well as apolipoproteins and glycerolipid synthesis enzymes that play a role in the assembly and secretion of apolipoprotein B100-containing very low density lipoproteins. Thus, the centrifugal proteomic reactor offers a new analytical tool for structure and function studies of membrane proteins involved in lipid and lipoprotein metabolism. PMID:21749988

Mitochondrial Proteome Studies in Seeds during Germination

PubMed Central

Czarna, Malgorzata; Kolodziejczak, Marta; Janska, Hanna

2016-01-01

Seed germination is considered to be one of the most critical phases in the plant life cycle, establishing the next generation of a plant species. It is an energy-demanding process that requires functioning mitochondria. One of the earliest events of seed germination is progressive development of structurally simple and metabolically quiescent promitochondria into fully active and cristae-containing mitochondria, known as mitochondrial biogenesis. This is a complex and tightly regulated process, which is accompanied by sequential and dynamic gene expression, protein synthesis, and post-translational modifications. The aim of this review is to give a comprehensive summary of seed mitochondrial proteome studies during germination of various plant model organisms. We describe different gel-based and gel-free proteomic approaches used to characterize mitochondrial proteomes of germinating seeds as well as challenges and limitations of these proteomic studies. Furthermore, the dynamic changes in the abundance of the mitochondrial proteomes of germinating seeds are illustrated, highlighting numerous mitochondrial proteins involved in respiration, tricarboxycylic acid (TCA) cycle, metabolism, import, and stress response as potentially important for seed germination. We then review seed mitochondrial protein carbonylation, phosphorylation, and S-nitrosylation as well as discuss the possible link between these post-translational modifications (PTMs) and the regulation of seed germination. PMID:28248229

Red blood cell (RBC) membrane proteomics--Part I: Proteomics and RBC physiology.

PubMed

Pasini, Erica M; Lutz, Hans U; Mann, Matthias; Thomas, Alan W

2010-01-03

Membrane proteomics is concerned with accurately and sensitively identifying molecules involved in cell compartmentalisation, including those controlling the interface between the cell and the outside world. The high lipid content of the environment in which these proteins are found often causes a particular set of problems that must be overcome when isolating the required material before effective HPLC-MS approaches can be performed. The membrane is an unusually dynamic cellular structure since it interacts with an ever changing environment. A full understanding of this critical cell component will ultimately require, in addition to proteomics, lipidomics, glycomics, interactomics and study of post-translational modifications. Devoid of nucleus and organelles in mammalian species other than camelids, and constantly in motion in the blood stream, red blood cells (RBCs) are the sole mammalian oxygen transporter. The fact that mature mammalian RBCs have no internal membrane-bound organelles, somewhat simplifies proteomics analysis of the plasma membrane and the fact that it has no nucleus disqualifies microarray based methods. Proteomics has the potential to provide a better understanding of this critical interface, and thereby assist in identifying new approaches to diseases. (c) 2009 Elsevier B.V. All rights reserved.

Five years later: the current status of the use of proteomics and transcriptomics in EMF research.

PubMed

Leszczynski, Dariusz; de Pomerai, David; Koczan, Dirk; Stoll, Dieter; Franke, Helmut; Albar, Juan Pablo

2012-08-01

The World Health Organization's and Radiation and Nuclear Safety Authority's "Workshop on Application of Proteomics and Transcriptomics in Electromagnetic Fields Research" was held in Helsinki in the October/November 2005. As a consequence of this meeting, Proteomics journal published in 2006 a special issue "Application of Proteomics and Transcriptomics in EMF Research" (Vol. 6 No. 17; Guest Editor: D. Leszczynski). This Proteomics issue presented the status of research, of the effects of electromagnetic fields (EMF) using proteomics and transcriptomics methods, present in 2005. The current overview/opinion article presents the status of research in this area by reviewing all studies that were published by the end of 2010. The review work was a part of the European Cooperation in the Field of Scientific and Technical Research (COST) Action BM0704 that created a structure in which researchers in the field of EMF and health shared knowledge and information. The review was prepared by the members of the COST Action BM0704 task group on the high-throughput screening techniques and electromagnetic fields (TG-HTST-EMF). © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Defining the extracellular matrix using proteomics

PubMed Central

Byron, Adam; Humphries, Jonathan D; Humphries, Martin J

2013-01-01

The cell microenvironment has a profound influence on the behaviour, growth and survival of cells. The extracellular matrix (ECM) provides not only mechanical and structural support to cells and tissues but also binds soluble ligands and transmembrane receptors to provide spatial coordination of signalling processes. The ability of cells to sense the chemical, mechanical and topographical features of the ECM enables them to integrate complex, multiparametric information into a coherent response to the surrounding microenvironment. Consequently, dysregulation or mutation of ECM components results in a broad range of pathological conditions. Characterization of the composition of ECM derived from various cells has begun to reveal insights into ECM structure and function, and mechanisms of disease. Proteomic methodologies permit the global analysis of subcellular systems, but extracellular and transmembrane proteins present analytical difficulties to proteomic strategies owing to the particular biochemical properties of these molecules. Here, we review advances in proteomic approaches that have been applied to furthering our understanding of the ECM microenvironment. We survey recent studies that have addressed challenges in the analysis of ECM and discuss major outcomes in the context of health and disease. In addition, we summarize efforts to progress towards a systems-level understanding of ECM biology. PMID:23419153

Experiences of Knowledge Brokering for Evidence-Informed Public Health Policy and Practice: Three Years of the Scottish Collaboration for Public Health Research and Policy

ERIC Educational Resources Information Center

Frost, Helen; Geddes, Rosemary; Haw, Sally; Jackson, Caroline A.; Jepson, Ruth; Mooney, John D.; Frank, John

2012-01-01

Despite a burgeoning literature on, and widespread interest in, knowledge translation and exchange in public health, few articles provide an account of the actual experiences of knowledge brokerage organisations. The Scottish Collaboration for Public Health Research and Policy (SCPHRP) was formed in 2008 to: identify public health interventions…

Wild harvests from Scottish woodlands: an exploration of the health and well-being of non-timber forest products collection and use

Treesearch

Suzanne Martin; Marla Emery; Alison Dyke

2005-01-01

Small-scale gathering of nontimber forest products (NTFPs) - wild edibles, medicinals, craft materials, etc. - has a range of benefits which have a specific bearing on the health and well-being of gatherers in contemporary Scottish society. The information discussed in this paper is drawn from qualitative research which focused on identifying and understanding the...

DRI Technical Program: Emerging Dynamics of the Marginal Ice Zone Ice, Ocean and Atmosphere Interactions in the Arctic Marginal Ice Zone. Year 3 Annual Report

DTIC Science & Technology

2014-09-30

Institution The Scottish Association for Marine Science tmaksym@whoi.edu Phil.Hwang@sams.ac.uk LONG-TERM GOALS This DRI TECHNICAL PROGRAM (Emerging...jpw28@bas.ac.uk tmaksym@whoi.edu Co-PRINCIPAL INVESTIGATOR: Byongjun (Phil) Hwang The Scottish Association for Marine Science Phil.Hwang@sams.ac.uk 2

Wild Harvests from Scottish Woodlands Social, cultural and economic values of contemporary non-timber forest products

Treesearch

Marla Emery; Suzanne Martin; Alison Dyke; Alison Dyke

2006-01-01

More than 30 people were interviewed about the wild edibles, medicinals, and craft materials they collect and the part that collecting plays in their lives as part of the Wild Harvests from Scottish Woodlands project. Interviews were conducted in autumn 2004. Collecting non-timber forest products (NTFPs) is a source of joy and satisfaction for many of those interviewed...

The Relationship between Waiting Times and "Adherence" to the Scottish Intercollegiate Guidelines Network 98 Guideline in Autism Spectrum Disorder Diagnostic Services in Scotland

ERIC Educational Resources Information Center

McKenzie, Karen; Forsyth, Kirsty; O'Hare, Anne; McClure, Iain; Rutherford, Marion; Murray, Aja; Irvine, Linda

2016-01-01

The aim of this study was to explore the extent to which the Scottish Intercollegiate Guidelines Network 98 guidelines on the assessment and diagnosis of autism spectrum disorder were adhered to in child autism spectrum disorder diagnostic services in Scotland and whether there was a significant relationship between routine practice which more…

Young People in Rural Scotland: Getting Out and Staying On. CES Briefing No. 13.

ERIC Educational Resources Information Center

Jones, Gill; Jamieson, Lynn

A study of youth out-migration from the Scottish Borders region was based on the 1989 Scottish Young People's Survey--a survey of students during their final compulsory school year (age 16-17)--plus followup interviews in 1995 with 23-year-olds from the rural Borders region. Among those in school in the Borders at age 16, only around one-third…

Early Professional Development in the Scottish Context: Pre-Service High School Teachers and the Management of Behaviour in Classrooms

ERIC Educational Resources Information Center

Hamilton, Lorna

2015-01-01

This paper gives an account of an exploratory piece of research focused on understanding more fully the nature of pre-service teachers' developing approaches to classroom behaviour management on a one-year postgraduate teacher education programme in the Scottish context. Drawing on individual and focus group interviews as well as journaling of…

"I like It Instead of Maths": How Pupils with Moderate Learning Difficulties in Scottish Primary Special Schools Intuitively Solved Mathematical Word Problems

ERIC Educational Resources Information Center

Moscardini, Lio

2010-01-01

This study by Lio Moscardini of the University of Strathclyde shows how a group of 24 children in three Scottish primary schools for pupils with moderate learning difficulties responded to word problems following their teachers' introduction to the principles of Cognitively Guided Instruction (CGI). CGI is a professional development programme in…

The Development of Learner Employability in Scotland's Colleges: A Thematic Aspect Report by Education Scotland on Behalf of the Scottish Funding Council

ERIC Educational Resources Information Center

Education Scotland, 2016

2016-01-01

This report is one of a suite of reports by Education Scotland commissioned by the Scottish Further and Higher Education Funding Council (SFC) to evaluate provision in colleges for supporting learner success. Colleges should act on the recommendations contained in these reports. College inspectors will monitor action towards implementation of…

Preserving the Social Cohesiveness and Lifelong Learning Mission of Scotland's Public Libraries: Evaluating the Scottish National Library Strategy through the Capabilities Approach

ERIC Educational Resources Information Center

Badwal, Kiran

2016-01-01

The following paper is based on my master's degree thesis written as a graduate student at the University of Glasgow from 2014-2015 titled, "Preserving the Social Cohesiveness and Lifelong Educational Mission of Public Libraries in Times of Austerity: Assessing the Potential of the Scottish National Library Strategy through the Capabilities…

Exploring the Work/Life/Study Balance: The Experience of Higher Education Students in a Scottish Further Education College

ERIC Educational Resources Information Center

Lowe, Janet; Gayle, Vernon

2007-01-01

This study explores the dimensions of the work/life/study balance and its influence on student participation in higher education, through a case study of the experience of higher education students, studying both full time and part time, in a Scottish further education college. The experience of the students and the work/life/study challenges that…

Does the 'Scottish effect' apply to all ethnic groups? All-cancer, lung, colorectal, breast and prostate cancer in the Scottish Health and Ethnicity Linkage Cohort Study.

PubMed

Bhopal, Raj S; Bansal, Narinder; Steiner, Markus; Brewster, David H

2012-01-01

Although ethnic group variations in cancer exist, no multiethnic, population-based, longitudinal studies are available in Europe. Our objectives were to examine ethnic variation in all-cancer, and lung, colorectal, breast and prostate cancers. DESIGN, SETTING, POPULATION, MEASURES AND ANALYSIS: This retrospective cohort study of 4.65 million people linked the 2001 Scottish Census (providing ethnic group) to cancer databases. With the White Scottish population as reference (value 100), directly age standardised rates and ratios (DASR and DASRR), and risk ratios, by sex and ethnic group with 95% CI were calculated for first cancers. In the results below, 95% CI around the DASRR excludes 100. Eight indicators of socio-economic position were assessed as potential confounders across all groups. For all cancers the White Scottish population (100) had the highest DASRRs, Indians the lowest (men 45.9 and women 41.2) and White British (men 87.6 and women 87.3) and other groups were intermediate (eg, Chinese men 57.6). For lung cancer the DASRRs for Pakistani men (45.0), and women (53.5), were low and for any mixed background men high (174.5). For colorectal cancer the DASRRs were lowest in Pakistanis (men 32.9 and women 68.9), White British (men 82.4 and women 83.7), other White (men 77.2 and women 74.9) and Chinese men (42.6). Breast cancer in women was low in Pakistanis (62.2), Chinese (63.0) and White Irish (84.0). Prostate cancer was lowest in Pakistanis (38.7), Indian (62.6) and White Irish (85.4). No socio-economic indicator was a valid confounding variable across ethnic groups. The 'Scottish effect' does not apply across ethnic groups for cancer. The findings have implications for clinical care, prevention and screening, for example, responding appropriately to the known low uptake among South Asian populations of bowel screening might benefit from modelling of cost-effectiveness of screening, given comparatively low cancer rates.

Does the ‘Scottish effect’ apply to all ethnic groups? All-cancer, lung, colorectal, breast and prostate cancer in the Scottish Health and Ethnicity Linkage Cohort Study

PubMed Central

Bhopal, Raj S; Bansal, Narinder; Steiner, Markus; Brewster, David H

2012-01-01

Background and objectives Although ethnic group variations in cancer exist, no multiethnic, population-based, longitudinal studies are available in Europe. Our objectives were to examine ethnic variation in all-cancer, and lung, colorectal, breast and prostate cancers. Design, setting, population, measures and analysis This retrospective cohort study of 4.65 million people linked the 2001 Scottish Census (providing ethnic group) to cancer databases. With the White Scottish population as reference (value 100), directly age standardised rates and ratios (DASR and DASRR), and risk ratios, by sex and ethnic group with 95% CI were calculated for first cancers. In the results below, 95% CI around the DASRR excludes 100. Eight indicators of socio-economic position were assessed as potential confounders across all groups. Results For all cancers the White Scottish population (100) had the highest DASRRs, Indians the lowest (men 45.9 and women 41.2) and White British (men 87.6 and women 87.3) and other groups were intermediate (eg, Chinese men 57.6). For lung cancer the DASRRs for Pakistani men (45.0), and women (53.5), were low and for any mixed background men high (174.5). For colorectal cancer the DASRRs were lowest in Pakistanis (men 32.9 and women 68.9), White British (men 82.4 and women 83.7), other White (men 77.2 and women 74.9) and Chinese men (42.6). Breast cancer in women was low in Pakistanis (62.2), Chinese (63.0) and White Irish (84.0). Prostate cancer was lowest in Pakistanis (38.7), Indian (62.6) and White Irish (85.4). No socio-economic indicator was a valid confounding variable across ethnic groups. Conclusions The ‘Scottish effect’ does not apply across ethnic groups for cancer. The findings have implications for clinical care, prevention and screening, for example, responding appropriately to the known low uptake among South Asian populations of bowel screening might benefit from modelling of cost-effectiveness of screening, given comparatively low cancer rates. PMID:23012329

MinOmics, an Integrative and Immersive Tool for Multi-Omics Analysis.

PubMed

Maes, Alexandre; Martinez, Xavier; Druart, Karen; Laurent, Benoist; Guégan, Sean; Marchand, Christophe H; Lemaire, Stéphane D; Baaden, Marc

2018-06-21

Proteomic and transcriptomic technologies resulted in massive biological datasets, their interpretation requiring sophisticated computational strategies. Efficient and intuitive real-time analysis remains challenging. We use proteomic data on 1417 proteins of the green microalga Chlamydomonas reinhardtii to investigate physicochemical parameters governing selectivity of three cysteine-based redox post translational modifications (PTM): glutathionylation (SSG), nitrosylation (SNO) and disulphide bonds (SS) reduced by thioredoxins. We aim to understand underlying molecular mechanisms and structural determinants through integration of redox proteome data from gene- to structural level. Our interactive visual analytics approach on an 8.3 m2 display wall of 25 MPixel resolution features stereoscopic three dimensions (3D) representation performed by UnityMol WebGL. Virtual reality headsets complement the range of usage configurations for fully immersive tasks. Our experiments confirm that fast access to a rich cross-linked database is necessary for immersive analysis of structural data. We emphasize the possibility to display complex data structures and relationships in 3D, intrinsic to molecular structure visualization, but less common for omics-network analysis. Our setup is powered by MinOmics, an integrated analysis pipeline and visualization framework dedicated to multi-omics analysis. MinOmics integrates data from various sources into a materialized physical repository. We evaluate its performance, a design criterion for the framework.

Oral Health and Risk of Arthritis in the Scottish Population: Results from the Scottish Health Survey.

PubMed

Abbood, Hadeel Mohammed; Cherukara, George; Pathan, Ejaz; Macfarlane, Tatiana V

2017-01-01

To investigate the link between self-reported oral health and arthritis in the Scottish population using data from the Scottish Health Survey. Data were available from 2008 to 2013 on self-reported arthritis, oral health conditions and oral hygiene habits from the Scottish Health Survey. Arthritis was defined in this survey by self-reported long standing illness, those who reported having arthritis, rheumatism and/or fibrositis. Oral conditions were defined by self-reported bleeding gums, toothache, biting difficulties and/or edentulousness. Oral hygiene habits were defined by self-reported brushing teeth and/or using dental floss on daily basis. Logistic regression was used for statistical analysis adjusted for age, gender, qualification, smoking and body mass index. Prevalence of self-reported arthritis was 9.3% (95% confidence interval [CI] = 9.03 to 9.57). Those who reported having bleeding gums (adjusted odds ratio [OR] = 1.63; 95% CI = 1.35 to 1.96), toothache (OR = 1.32; 95% CI = 1.16 to 1.5), biting difficulties (OR = 1.95; 95% CI = 1.62 to 2.34), and being edentulous (OR = 1.22; 95% CI = 1.08 to 1.37) had an increased risk of arthritis. Brushing teeth (OR = 1.25; 95% CI = 0.74 to 2.12), and using dental floss (OR = 1.11; 95% CI = 0.89 to 1.39) were not associated with arthritis. Self-reported oral conditions were associated with increased risk of self-reported arthritis. Oral hygiene habits were not associated with self-reported arthritis. Further investigation is required to assess the causal association between oral hygiene, oral disease and arthritis.

A dominant TRPV4 variant underlies osteochondrodysplasia in Scottish fold cats.

PubMed

Gandolfi, B; Alamri, S; Darby, W G; Adhikari, B; Lattimer, J C; Malik, R; Wade, C M; Lyons, L A; Cheng, J; Bateman, J F; McIntyre, P; Lamandé, S R; Haase, B

2016-08-01

Scottish fold cats, named for their unique ear shape, have a dominantly inherited osteochondrodysplasia involving malformation in the distal forelimbs, distal hindlimbs and tail, and progressive joint destruction. This study aimed to identify the gene and the underlying variant responsible for the osteochondrodysplasia. DNA samples from 44 Scottish fold and 54 control cats were genotyped using a feline DNA array and a case-control genome-wide association analysis conducted. The gene encoding a calcium permeable ion channel, transient receptor potential cation channel, subfamily V, member 4 (TRPV4) was identified as a candidate within the associated region and sequenced. Stably transfected HEK293 cells were used to compare wild-type and mutant TRPV4 expression, cell surface localisation and responses to activation with a synthetic agonist GSK1016709A, hypo-osmolarity, and protease-activated receptor 2 stimulation. The dominantly inherited folded ear and osteochondrodysplasia in Scottish fold cats is associated with a p.V342F substitution (c.1024G>T) in TRPV4. The change was not found in 648 unaffected cats. Functional analysis in HEK293 cells showed V342F mutant TRPV4 was poorly expressed at the cell surface compared to wild-type TRPV4 and as a consequence the maximum response to a synthetic agonist was reduced. Mutant TRPV4 channels had a higher basal activity and an increased response to hypotonic conditions. Access to a naturally-occurring TRPV4 mutation in the Scottish fold cat will allow further functional studies to identify how and why the mutations affect cartilage and bone development. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

The epidemiology of adults with severe sepsis and septic shock in Scottish emergency departments.

PubMed

Gray, Alasdair; Ward, Kirsty; Lees, Fiona; Dewar, Colin; Dickie, Sarah; McGuffie, Crawford

2013-05-01

The Surviving Sepsis Campaign (SSC) promotes a bundle approach to the care of septic patients to improve outcome. Some have questioned the capability of delivering the bundle in emergency departments (EDs). The authors report the epidemiology and 6 h bundle compliance of patients with severe sepsis/septic shock presenting to Scottish EDs. Analysis of the previously reported Scottish Trauma Audit Group sepsis database was performed including 20 mainland Scottish EDs. A total of 308,910 attendances were screened (between 2 March and 31 May 2009), and 5285 of 27,046 patients were identified after case note review and included on the database. This analysis includes patients who had severe sepsis/septic shock before leaving the ED. Epidemiological, severity of illness criteria, and ED management data were analysed. 626 patients (median age 73; M/F ratio 1:1; 637 presentations) met entrance criteria. The median number of cases per site was 16 (range 3-103). 561 (88.1%) patients arrived by ambulance. The most common source of infection was the respiratory tract (n=411, 64.5%) The most common physiological derangements were heart rate (n=523, 82.1%), respiratory rate (n=452, 71%) and white cell count (n=432, 67.8%). The median hospital stay was 9 days (IQR 4-17 days). 201 (31.6%) patients were admitted to critical care within 2 days, 130 (20.4%) directly from the ED. 180 patients (28.3%) died. There was poor compliance with all aspect of the SSC resuscitation bundle. Sepsis presentations are of variable frequency but have typical epidemiology and clinical outcomes. SSC bundle resuscitation uptake is poor in Scottish EDs.

HPV immunisation and increased uptake of cervical screening in Scottish women; observational study of routinely collected national data.

PubMed

Palmer, T J; McFadden, M; Pollock, K G J; Kavanagh, K; Cuschieri, K; Cruickshank, M; Nicoll, S; Robertson, C

2016-03-01

To measure the uptake of first invitation to cervical screening by vaccine status in a population-based cohort offered HPV immunisation in a national catch-up campaign. A retrospective observational study of routinely collected data from the Scottish Cervical Screening Programme. Data were extracted and linked from the Scottish Cervical Call Recall System, the Scottish Population Register and the Scottish Index of Multiple Deprivation. Records from 201 023 women born between 1 January 1988 and 30 September 1993 were assessed. Women born in or after 1990 were eligible for the national catch-up programme of HPV immunisation. Attendance for screening was within 12 months of the first invitation at age 20 years. There was a significant decline in overall attendance from the 1988 cohort to the 1993 cohort with the adjusted attendance ratio of the 1988 cohort being 1.49 times (95% CI 1.46-1.52) that of the 1993 cohort. Immunisation compensated for this decrease in uptake with unvaccinated individuals having a reduced ratio of attendance compared with those fully vaccinated (RR=0.65, 95% CI 0.64-0.65). Not taking up the opportunity for HPV immunisation was associated with an attendance for screening below the trend line for all women before the availability of HPV immunisation. HPV immunisation is not associated with the reduced attendance for screening that had been feared. Immunised women in the catch-up cohorts appear to be more motivated to attend than unimmunised women, but this may be a result of a greater awareness of health issues. These results, while reassuring, may not be reproduced in routinely immunised women. Continued monitoring of attendance for the first smear and subsequent routine smears is needed.

Comparing early years and childhood experiences and outcomes in Scotland, England and three city-regions: a plausible explanation for Scottish 'excess' mortality?

PubMed

Taulbut, Martin; Walsh, David; O'Dowd, John

2014-10-10

Negative early years and childhood experiences (EYCE), including socio-economic circumstances, parental health and parenting style, are associated with poor health outcomes both in childhood and adulthood. It has also been proposed that EYCE were historically worse in Scottish areas, especially Glasgow and the Clyde Valley, compared to elsewhere in the UK and that this variation can provide a partial explanation for the excess of ill health and mortality observed among those Scottish populations. Multiple logistic regression analysis was applied to two large, representative, British birth cohorts (the NCDS58 and the BCS70), to test the independent association of area of residence at ages 7 and 5 with risk of behavioural problems, respiratory problems and reading/vocabulary problems at the same age. Cohort members resident in Scotland were compared with those who were resident in England, while those resident in Glasgow and the Clyde Valley were compared with those resident in Merseyside and Greater Manchester. After adjustment for a range of relevant variables, the risk of adverse childhood outcomes was found to be either no different, or lower, in the Scottish areas. At a national level, the study reinforces the combined association of socio-economic circumstances, parental health (especially maternal mental health) and parenting with child health outcomes. Based on these samples, the study does not support the hypothesis that EYCE were worse in Scotland and Glasgow and the Clyde Valley. It seems, therefore (based on these data), less likely that the roots of the excess mortality observed in the Scottish areas can be explained by these factors.

Elucidating structural and molecular mechanisms of β-arrestin-biased agonism at GPCRs via MS-based proteomics.

PubMed

Xiao, Kunhong; Sun, Jinpeng

2018-01-01

The discovery of β-arrestin-dependent GPCR signaling has led to an exciting new field in GPCR pharmacology: to develop "biased agonists" that can selectively target a specific downstream signaling pathway that elicits beneficial therapeutic effects without activating other pathways that elicit negative side effects. This new trend in GPCR drug discovery requires us to understand the structural and molecular mechanisms of β-arrestin-biased agonism, which largely remain unclear. We have used cutting-edge mass spectrometry (MS)-based proteomics, combined with systems, chemical and structural biology to study protein function, macromolecular interaction, protein expression and posttranslational modifications in the β-arrestin-dependent GPCR signaling. These high-throughput proteomic studies have provided a systems view of β-arrestin-biased agonism from several perspectives: distinct receptor phosphorylation barcode, multiple receptor conformations, distinct β-arrestin conformations, and ligand-specific signaling. The information obtained from these studies offers new insights into the molecular basis of GPCR regulation by β-arrestin and provides a potential platform for developing novel therapeutic interventions through GPCRs. Copyright © 2017 Elsevier Inc. All rights reserved.

The proteome of the wool cuticle.

PubMed

Koehn, Henning; Clerens, Stefan; Deb-Choudhury, Santanu; Morton, James D; Dyer, Jolon M; Plowman, Jeffrey E

2010-06-04

The cuticle is responsible for important wool fiber characteristics such as handle and abrasion resistance, which impact on the fiber's performance in both interior and apparel textiles. The cuticle proteome, however, is not well understood due to the difficulty in isolating pure wool cuticle and its significant resistance to protein extraction, which is attributed to the presence of extensive disulfide and isopeptide cross-linking. We investigated the proteome of highly pure Merino wool cuticle using a combined strategy of chemical and enzymatic digestion and identified 108 proteins, including proteins responsible for a variety of cellular processes. The majority of identified proteins belonged to keratin and nonkeratin protein families known to play an important role in molecular assembly and cellular structure. Keratin-associated, intermediate filament and cytoskeletal keratin proteins were identified as the most prominent keratinous cuticular constituents, while histones, tubulins, and desmosomes were the key nonkeratin structural proteins. We conclude that a variety of proteins contribute to cuticle structure and fiber characteristics, and that the keratinous protein families of IFPs and KAPs represent the most important cuticular constituents.

The mine management professions in the twentieth-century Scottish coal mining industry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perchard, A.

2007-07-01

This book seeks to redress the exclusion of colliery managers and other mining professionals from the history of British, and particularly Scottish, coal industries. This is accomplished by examining these groups within the most crucial period of their ascendancy in the Scottish coal mining industry, 1930-1966. This work seeks to place such persons within their context and to examine their roles, statuses and behaviours through their relationships with employees and the execution of their functions, also examining their terms and conditions of employment, the outlook of their professional associations, and that of their union. Through all this, Dr. Perchard illustratesmore » how this growing consciousness amongst managerial employees in the industry was accompanied by an intense public discussion, within the mining professions, over their future shape, principles and occupational standards.« less

The day/night proteome in the murine heart.

PubMed

Podobed, Peter; Pyle, W Glen; Ackloo, Suzanne; Alibhai, Faisal J; Tsimakouridze, Elena V; Ratcliffe, William F; Mackay, Allison; Simpson, Jeremy; Wright, David C; Kirby, Gordon M; Young, Martin E; Martino, Tami A

2014-07-15

Circadian rhythms are essential to cardiovascular health and disease. Temporal coordination of cardiac structure and function has focused primarily at the physiological and gene expression levels, but these analyses are invariably incomplete, not the least because proteins underlie many biological processes. The purpose of this study was to reveal the diurnal cardiac proteome and important contributions to cardiac function. The 24-h day-night murine cardiac proteome was assessed by two-dimensional difference in gel electrophoresis (2D-DIGE) and liquid chromatography-mass spectrometry. Daily variation was considerable, as ∼7.8% (90/1,147) of spots exhibited statistical changes at paired times across the 24-h light- (L) dark (D) cycle. JTK_CYCLE was used to investigate underlying diurnal rhythms in corresponding mRNA. We next revealed that disruption of the L:D cycle altered protein profiles and diurnal variation in cardiac function in Langendorff-perfused hearts, relative to the L:D cycle. To investigate the role of the circadian clock mechanism, we used cardiomyocyte clock mutant (CCM) mice. CCM myofilaments exhibited a loss of time-of-day-dependent maximal calcium-dependent ATP consumption, and altered phosphorylation rhythms. Moreover, the cardiac proteome was significantly altered in CCM hearts, especially enzymes regulating vital metabolic pathways. Lastly, we used a model of pressure overload cardiac hypertrophy to demonstrate the temporal proteome during heart disease. Our studies demonstrate that time of day plays a direct role in cardiac protein abundance and indicate a novel mechanistic contribution of circadian biology to cardiovascular structure and function.

The day/night proteome in the murine heart

PubMed Central

Podobed, Peter; Pyle, W. Glen; Ackloo, Suzanne; Alibhai, Faisal J.; Tsimakouridze, Elena V.; Ratcliffe, William F.; Mackay, Allison; Simpson, Jeremy; Wright, David C.; Kirby, Gordon M.; Young, Martin E.

2014-01-01

Circadian rhythms are essential to cardiovascular health and disease. Temporal coordination of cardiac structure and function has focused primarily at the physiological and gene expression levels, but these analyses are invariably incomplete, not the least because proteins underlie many biological processes. The purpose of this study was to reveal the diurnal cardiac proteome and important contributions to cardiac function. The 24-h day-night murine cardiac proteome was assessed by two-dimensional difference in gel electrophoresis (2D-DIGE) and liquid chromatography-mass spectrometry. Daily variation was considerable, as ∼7.8% (90/1,147) of spots exhibited statistical changes at paired times across the 24-h light- (L) dark (D) cycle. JTK_CYCLE was used to investigate underlying diurnal rhythms in corresponding mRNA. We next revealed that disruption of the L:D cycle altered protein profiles and diurnal variation in cardiac function in Langendorff-perfused hearts, relative to the L:D cycle. To investigate the role of the circadian clock mechanism, we used cardiomyocyte clock mutant (CCM) mice. CCM myofilaments exhibited a loss of time-of-day-dependent maximal calcium-dependent ATP consumption, and altered phosphorylation rhythms. Moreover, the cardiac proteome was significantly altered in CCM hearts, especially enzymes regulating vital metabolic pathways. Lastly, we used a model of pressure overload cardiac hypertrophy to demonstrate the temporal proteome during heart disease. Our studies demonstrate that time of day plays a direct role in cardiac protein abundance and indicate a novel mechanistic contribution of circadian biology to cardiovascular structure and function. PMID:24789993

Business, Management and Administration: A Subject-Based Aspect Report by Education Scotland on Behalf of the Scottish Funding Council on Provision in Scotland's Colleges. Transforming Lives through Learning

ERIC Educational Resources Information Center

Education Scotland, 2014

2014-01-01

In preparing this report, reviewers visited a sample of four colleges, detailed in Appendix 1. They also drew on the findings of published Education Scotland external reviews of colleges, and examined other relevant publications and reports. They consulted and held focus groups with key stakeholders, including the Scottish Qualifications Authority…

Choice of Scottish Gaelic-Medium and Welsh-Medium Education at the Primary and Secondary School Stages: Parent and Pupil Perspectives

ERIC Educational Resources Information Center

O'Hanlon, Fiona

2015-01-01

Results are presented of a comparative study of the reasons for parental choice of Scottish Gaelic-medium and Welsh-medium primary education in the year 2000 and of the reasons for pupils' decisions to continue with Gaelic or Welsh-medium education at secondary school in 2007. Parents in both contexts cited the quality of Celtic-medium education…

Pupils' Perceptions of and Experiences in Team Invasion Games: A Case Study of a Scottish Secondary School and Its Three Feeder Primary Schools

ERIC Educational Resources Information Center

Gray, Shirley; Sproule, John; Wang, C. K. John

2008-01-01

It has been claimed that young children in schools in Scotland cannot relate to the activities that are taught in the more "traditional" PE curriculum, activities that predominately include team invasion games (TIG) such as basketball, soccer and hockey (Scottish Executive, 2004). However, one of the issues with this claim is that it…

Social deprivation and prognosis in Scottish patients with pulmonary arterial hypertension.

PubMed

Pellino, Katherine; Kerridge, Simon; Church, Colin; Peacock, Andrew J; Crowe, Timothy; Jayasekera, Geeshath; Johnson, Martin K; MacKenzie, Alison M

2018-02-01

Several demographic and clinical factors have prognostic significance in idiopathic pulmonary arterial hypertension (IPAH). Studies in China and the USA have suggested an association between low socioeconomic status and reduced survival. The impact of social deprivation on IPAH survival in the UK is not known.280 patients with IPAH and hereditary PAH (HPAH) attending the Scottish Pulmonary Vascular Unit (Glasgow, UK) were assigned to social deprivation quintiles using the Scottish Index of Multiple Deprivation database. The association between survival and social deprivation quintile was assessed using Cox proportional hazards regression analysis.The distribution of IPAH/HPAH patients was more socially deprived than would be expected based on Scottish citizenry as a whole (Chi-squared 16.16, p=0.003), suggesting referral and access to care is not impeded by socioeconomic status. Univariate analysis demonstrated no significant association between social deprivation and survival (p=0.81), and this association failed to reach significance with inclusion of time, sex and age as covariates in the model (p=0.23). There were no statistically significant correlations between social deprivation and baseline clinical variables of prognostic importance except for age, sex and quality of life.Social deprivation is not a significant referral barrier or prognostic factor for IPAH and HPAH in Scotland. Copyright ©ERS 2018.

Glaucoma-service provision in Scotland: introduction and need for Scottish Intercollegiate Guidelines Network guidelines.

PubMed

Syrogiannis, Andreas; Rotchford, Alan P; Agarwal, Pankaj Kumar; Kumarasamy, Manjula; Montgomery, Donald; Burr, Jennifer; Sanders, Roshini

2015-01-01

To describe the pattern of glaucoma-service delivery in Scotland and identify areas for improvement, taking into account Scottish General Ophthalmic Services (GOS) arrangements and the Eye Care Integration project, and to design Scottish Intercollegiate Guidelines Network (SIGN) guidelines to refine the primary and secondary interface of glaucoma care. A glaucoma-survey questionnaire was sent to all consultant glaucomatologists in Scotland. The design of SIGN guidelines was based on the results of the questionnaire using SIGN methodology. Over 90% of Scottish glaucoma care is triaged and delivered within hospital services. Despite GOS referral, information is variable. There are no consistent discharge practices to the community. These results led to defined research questions that were answered, thus formulating the content of the SIGN guidelines. The guideline covers the assessment of patients in primary care, referral criteria to hospital, discharge criteria from hospital to community, and monitoring of patients at risk of glaucoma. With increasing age and limitations to hospital resources, refining glaucoma pathways between primary and secondary care has become a necessity. Scotland has unique eye care arrangements with both the GOS and Eye Care Integration project. It is hoped that implementation of SIGN guidelines will identify glaucoma at the earliest opportunity and reduce the rate of false-positive referrals to hospital.

Pathways between Socioeconomic Disadvantage and Childhood Growth in the Scottish Longitudinal Study, 1991-2001.

PubMed

Silverwood, Richard J; Williamson, Lee; Grundy, Emily M; De Stavola, Bianca L

2016-01-01

Socioeconomically disadvantaged children are more likely to be of shorter stature and overweight, leading to greater risk of obesity in adulthood. Disentangling the mediatory pathways between socioeconomic disadvantage and childhood size may help in the development of appropriate policies aimed at reducing these health inequalities. We aimed to elucidate the putative mediatory role of birth weight using a representative sample of the Scottish population born 1991-2001 (n = 16,628). Estimated height and overweight/obesity at age 4.5 years were related to three measures of socioeconomic disadvantage (mother's education, Scottish Index of Multiple Deprivation, synthetic weekly income). Mediation was examined using two approaches: a 'traditional' mediation analysis and a counterfactual-based mediation analysis. Both analyses identified a negative effect of each measure of socioeconomic disadvantage on height, mediated to some extent by birth weight, and a positive 'direct effect' of mother's education and Scottish Index of Multiple Deprivation on overweight/obesity, which was partly counterbalanced by a negative 'indirect effect'. The extent of mediation estimated when adopting the traditional approach was greater than when adopting the counterfactual-based approach because of inappropriate handling of intermediate confounding in the former. Our findings suggest that higher birth weight in more disadvantaged groups is associated with reduced social inequalities in height but also with increased inequalities in overweight/obesity.

Navigating future uncertainty in marine protected area governance: Lessons from the Scottish MPA network

NASA Astrophysics Data System (ADS)

Hopkins, Charlotte Rachael; Bailey, David Mark; Potts, Tavis

2018-07-01

As international pressure for marine protection has increased, Scotland has increased spatial protection through the development of a Marine Protected Area (MPA) network. Few MPA networks to date have included specific considerations of climate change in the design, monitoring or management of the network. The Scottish MPA network followed a feature-led approach to identify a series of MPAs across the Scottish marine area and incorporated the diverse views of many different stakeholders. This feature led approach has led to wide ranging opinions and understandings regarding the success of the MPA network. Translating ideas of success into a policy approach whilst also considering how climate change may affect these ideas of success is a complex challenge. This paper presents the results of a Delphi process that aimed to facilitate clear communication between academics, policy makers and stakeholders in order to identify specific climate change considerations applicable to the Scottish MPA network. This study engaged a group of academic and non-academic stakeholders to discuss potential options that could be translated into an operational process for management of the MPA network. The results of Delphi process discussion are presented with the output of a management matrix tool, which could aid in future decisions for MPA management under scenarios of climate change.

Integrating Mass Spectrometry of Intact Protein Complexes into Structural Proteomics

PubMed Central

Hyung, Suk-Joon; Ruotolo, Brandon T.

2013-01-01

Summary Mass spectrometry analysis of intact protein complexes has emerged as an established technology for assessing the composition and connectivity within dynamic, heterogeneous multiprotein complexes at low concentrations and in the context of mixtures. As this technology continues to move forward, one of the main challenges is to integrate the information content of such intact protein complex measurements with other mass spectrometry approaches in structural biology. Methods such as H/D exchange, oxidative foot-printing, chemical cross-linking, affinity purification, and ion mobility separation add complementary information that allows access to every level of protein structure and organization. Here, we survey the structural information that can be retrieved by such experiments, demonstrate the applicability of integrative mass spectrometry approaches in structural proteomics, and look to the future to explore upcoming innovations in this rapidly-advancing area. PMID:22611037

The diverse and expanding role of mass spectrometry in structural and molecular biology.

PubMed

Lössl, Philip; van de Waterbeemd, Michiel; Heck, Albert Jr

2016-12-15

The emergence of proteomics has led to major technological advances in mass spectrometry (MS). These advancements not only benefitted MS-based high-throughput proteomics but also increased the impact of mass spectrometry on the field of structural and molecular biology. Here, we review how state-of-the-art MS methods, including native MS, top-down protein sequencing, cross-linking-MS, and hydrogen-deuterium exchange-MS, nowadays enable the characterization of biomolecular structures, functions, and interactions. In particular, we focus on the role of mass spectrometry in integrated structural and molecular biology investigations of biological macromolecular complexes and cellular machineries, highlighting work on CRISPR-Cas systems and eukaryotic transcription complexes. © 2016 The Authors. Published under the terms of the CC BY NC ND 4.0 license.

Advancing Cell Biology Through Proteomics in Space and Time (PROSPECTS)*

PubMed Central

Lamond, Angus I.; Uhlen, Mathias; Horning, Stevan; Makarov, Alexander; Robinson, Carol V.; Serrano, Luis; Hartl, F. Ulrich; Baumeister, Wolfgang; Werenskiold, Anne Katrin; Andersen, Jens S.; Vorm, Ole; Linial, Michal; Aebersold, Ruedi; Mann, Matthias

2012-01-01

The term “proteomics” encompasses the large-scale detection and analysis of proteins and their post-translational modifications. Driven by major improvements in mass spectrometric instrumentation, methodology, and data analysis, the proteomics field has burgeoned in recent years. It now provides a range of sensitive and quantitative approaches for measuring protein structures and dynamics that promise to revolutionize our understanding of cell biology and molecular mechanisms in both human cells and model organisms. The Proteomics Specification in Time and Space (PROSPECTS) Network is a unique EU-funded project that brings together leading European research groups, spanning from instrumentation to biomedicine, in a collaborative five year initiative to develop new methods and applications for the functional analysis of cellular proteins. This special issue of Molecular and Cellular Proteomics presents 16 research papers reporting major recent progress by the PROSPECTS groups, including improvements to the resolution and sensitivity of the Orbitrap family of mass spectrometers, systematic detection of proteins using highly characterized antibody collections, and new methods for absolute as well as relative quantification of protein levels. Manuscripts in this issue exemplify approaches for performing quantitative measurements of cell proteomes and for studying their dynamic responses to perturbation, both during normal cellular responses and in disease mechanisms. Here we present a perspective on how the proteomics field is moving beyond simply identifying proteins with high sensitivity toward providing a powerful and versatile set of assay systems for characterizing proteome dynamics and thereby creating a new “third generation” proteomics strategy that offers an indispensible tool for cell biology and molecular medicine. PMID:22311636

Secreted autoantibody repertoires in Sjögren's syndrome and systemic lupus erythematosus: A proteomic approach.

PubMed

Al Kindi, Mahmood A; Colella, Alex D; Chataway, Tim K; Jackson, Michael W; Wang, Jing J; Gordon, Tom P

2016-04-01

The structures of epitopes bound by autoantibodies against RNA-protein complexes have been well-defined over several decades, but little is known of the clonality, immunoglobulin (Ig) variable (V) gene usage and mutational status of the autoantibodies themselves at the level of the secreted (serum) proteome. A novel proteomic workflow is presented based on affinity purification of specific Igs from serum, high-resolution two-dimensional gel electrophoresis, and de novo and database-driven sequencing of V-region proteins by mass spectrometry. Analysis of anti-Ro52/Ro60/La proteomes in primary Sjögren's syndrome (SS) and anti-Sm and anti-ribosomal P proteomes in systemic lupus erythematosus (SLE) has revealed that these antibody responses are dominated by restricted sets of public (shared) clonotypes, consistent with common pathways of production across unrelated individuals. The discovery of shared sets of specific V-region peptides can be exploited for diagnostic biomarkers in targeted mass spectrometry platforms and for tracking and removal of pathogenic clones. Copyright © 2016 Elsevier B.V. All rights reserved.

Differential proteome analysis of diabetes mellitus type 2 and its pathophysiological complications.

PubMed

Sohail, Waleed; Majeed, Fatimah; Afroz, Amber

2018-06-11

The prevalence of Diabetes Mellitus Type 2 (DM 2) is increasing every passing year due to some global changes in lifestyles of people. The exact underlying mechanisms of the progression of this disease are not yet known. However recent advances in the combined omics more particularly in proteomics and genomics have opened a gateway towards the understanding of predetermined genetic factors, progression, complications and treatment of this disease. Here we shall review the recent advances in proteomics that have led to an early and better diagnostic approaches in controlling DM 2 more importantly the comparison of structural and functional protein biomarkers that are modified in the diseased state. By applying these advanced and promising proteomic strategies with bioinformatics applications and bio-statistical tools the prevalence of DM 2 and its associated disorders i-e nephropathy and retinopathy are expected to be controlled. Copyright © 2018 Diabetes India. Published by Elsevier Ltd. All rights reserved.

Combined metabolome and proteome analysis of the mantle tissue from Pacific oyster Crassostrea gigas exposed to elevated pCO2.

PubMed

Wei, Lei; Wang, Qing; Ning, Xuanxuan; Mu, Changkao; Wang, Chunlin; Cao, Ruiwen; Wu, Huifeng; Cong, Ming; Li, Fei; Ji, Chenglong; Zhao, Jianmin

2015-03-01

Ocean acidification (OA) has been found to affect an array of normal physiological processes in mollusks, especially posing a significant threat to the fabrication process of mollusk shell. In the current study, the impact of exposure to elevated pCO2 condition was investigated in mantle tissue of Crassostrea gigas by an integrated metabolomic and proteomic approach. Analysis of metabolome and proteome revealed that elevated pCO2 could affect energy metabolism in oyster C. gigas, marked by differentially altered ATP, succinate, MDH, PEPCK and ALDH levels. Moreover, the up-regulated calponin-2, tropomyosins and myosin light chains indicated that elevated pCO2 probably caused disturbances in cytoskeleton structure in mantle tissue of oyster C. gigas. This work demonstrated that a combination of proteomics and metabolomics could provide important insights into the effects of OA at molecular levels. Copyright © 2014 Elsevier Inc. All rights reserved.

Proteomics Analysis of Alfalfa Response to Heat Stress

PubMed Central

Li, Weimin; Wei, Zhenwu; Qiao, Zhihong; Wu, Zinian; Cheng, Lixiang; Wang, Yuyang

2013-01-01

The proteome responses to heat stress have not been well understood. In this study, alfalfa (Medicago sativa L. cv. Huaiyin) seedlings were exposed to 25°C (control) and 40°C (heat stress) in growth chambers, and leaves were collected at 24, 48 and 72 h after treatment, respectively. The morphological, physiological and proteomic processes were negatively affected under heat stress. Proteins were extracted and separated by two-dimensional polyacrylamide gel electrophoresis (2-DE), and differentially expressed protein spots were identified by mass spectrometry (MS). Totally, 81 differentially expressed proteins were identified successfully by MALDI-TOF/TOF. These proteins were categorized into nine classes: including metabolism, energy, protein synthesis, protein destination/storage, transporters, intracellular traffic, cell structure, signal transduction and disease/defence. Five proteins were further analyzed for mRNA levels. The results of the proteomics analyses provide a better understanding of the molecular basis of heat-stress responses in alfalfa. PMID:24324825

Redox Proteomics of Protein-bound Methionine Oxidation*

PubMed Central

Ghesquière, Bart; Jonckheere, Veronique; Colaert, Niklaas; Van Durme, Joost; Timmerman, Evy; Goethals, Marc; Schymkowitz, Joost; Rousseau, Frederic; Vandekerckhove, Joël; Gevaert, Kris

2011-01-01

We here present a new method to measure the degree of protein-bound methionine sulfoxide formation at a proteome-wide scale. In human Jurkat cells that were stressed with hydrogen peroxide, over 2000 oxidation-sensitive methionines in more than 1600 different proteins were mapped and their extent of oxidation was quantified. Meta-analysis of the sequences surrounding the oxidized methionine residues revealed a high preference for neighboring polar residues. Using synthetic methionine sulfoxide containing peptides designed according to the observed sequence preferences in the oxidized Jurkat proteome, we discovered that the substrate specificity of the cellular methionine sulfoxide reductases is a major determinant for the steady-state of methionine oxidation. This was supported by a structural modeling of the MsrA catalytic center. Finally, we applied our method onto a serum proteome from a mouse sepsis model and identified 35 in vivo methionine oxidation events in 27 different proteins. PMID:21406390

Maillard Proteomics: Opening New Pages

PubMed Central

Soboleva, Alena; Schmidt, Rico; Vikhnina, Maria; Grishina, Tatiana; Frolov, Andrej

2017-01-01

Protein glycation is a ubiquitous non-enzymatic post-translational modification, formed by reaction of protein amino and guanidino groups with carbonyl compounds, presumably reducing sugars and α-dicarbonyls. Resulting advanced glycation end products (AGEs) represent a highly heterogeneous group of compounds, deleterious in mammals due to their pro-inflammatory effect, and impact in pathogenesis of diabetes mellitus, Alzheimer’s disease and ageing. The body of information on the mechanisms and pathways of AGE formation, acquired during the last decades, clearly indicates a certain site-specificity of glycation. It makes characterization of individual glycation sites a critical pre-requisite for understanding in vivo mechanisms of AGE formation and developing adequate nutritional and therapeutic approaches to reduce it in humans. In this context, proteomics is the methodology of choice to address site-specific molecular changes related to protein glycation. Therefore, here we summarize the methods of Maillard proteomics, specifically focusing on the techniques providing comprehensive structural and quantitative characterization of glycated proteome. Further, we address the novel break-through areas, recently established in the field of Maillard research, i.e., in vitro models based on synthetic peptides, site-based diagnostics of metabolism-related diseases (e.g., diabetes mellitus), proteomics of anti-glycative defense, and dynamics of plant glycated proteome during ageing and response to environmental stress. PMID:29231845

Microbial Interactions in Plants: Perspectives and Applications of Proteomics.

PubMed

Imam, Jahangir; Shukla, Pratyoosh; Mandal, Nimai Prasad; Variar, Mukund

2017-01-01

The structure and function of proteins involved in plant-microbe interactions is investigated through large-scale proteomics technology in a complex biological sample. Since the whole genome sequences are now available for several plant species and microbes, proteomics study has become easier, accurate and huge amount of data can be generated and analyzed during plant-microbe interactions. Proteomics approaches are highly important and relevant in many studies and showed that only genomics approaches are not sufficient enough as much significant information are lost as the proteins and not the genes coding them are final product that is responsible for the observed phenotype. Novel approaches in proteomics are developing continuously enabling the study of the various aspects in arrangements and configuration of proteins and its functions. Its application is becoming more common and frequently used in plant-microbe interactions with the advancement in new technologies. They are more used for the portrayal of cell and extracellular destructiveness and pathogenicity variables delivered by pathogens. This distinguishes the protein level adjustments in host plants when infected with pathogens and advantageous partners. This review provides a brief overview of different proteomics technology which is currently available followed by their exploitation to study the plant-microbe interaction. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Utility of the PRE-DELIRIC delirium prediction model in a Scottish ICU cohort.

PubMed

Paton, Lia; Elliott, Sara; Chohan, Sanjiv

2016-08-01

The PREdiction of DELIRium for Intensive Care (PRE-DELIRIC) model reliably predicts at 24 h the development of delirium during intensive care admission. However, the model does not take account of alcohol misuse, which has a high prevalence in Scottish intensive care patients. We used the PRE-DELIRIC model to calculate the risk of delirium for patients in our ICU from May to July 2013. These patients were screened for delirium on each day of their ICU stay using the Confusion Assessment Method for ICU (CAM-ICU). Outcomes were ascertained from the national ICU database. In the 39 patients screened daily, the risk of delirium given by the PRE-DELIRIC model was positively associated with prevalence of delirium, length of ICU stay and mortality. The PRE-DELIRIC model can therefore be usefully applied to a Scottish cohort with a high prevalence of substance misuse, allowing preventive measures to be targeted.

A review of photodiagnostic investigations over 26 years: experience of the National Scottish Photobiology Service (1989-2015).

PubMed

Nassan, H; Dawe, R S; Moseley, H; Ibbotson, S H

2017-12-01

Background The Scottish Photobiology Service is the national referral pathway for patients with cutaneous photosensitivity diseases in Scotland. We reviewed the pattern of diagnosis of photosensitivity diseases and investigations performed between 1989 and 2015. Methods and Results Data were collected from the Photodiagnostic Database, annual reports and paper records. The total number of patients assessed each year was stable over the period studied (median 242 [range 231-266]), with most being new patients (median 69 [range 62-73]%). Monochromator phototesting was the most utilised investigation, although the use of provocation testing and photopatch testing has increased. The most common diagnosis was polymorphic light eruption, and there was a trend to increasing diagnosis of photoaggravated atopic eczema. Conclusions The pattern of diagnosis of photosensitivity diseases remains fairly stable in Scotland and we wish to emphasise the importance of this Scottish specialist service for patients with photosensitivity diseases and referrers.

Indicator-based systems of performance management in the National Health Service: a comparison of the perceptions of local- and national-level managers.

PubMed

Jones, G T

2000-02-01

Historically, the UK Government has policed the use of National Health Service (NHS) resources through the centralization of control. With the majority of resource-draining decisions being taken by clinicians, however, professional financial accountability is becoming more important within the NHS management structure. Variations in clinical performance can be monitored through the use of performance indicators, although these are not without their problems. The use of league tables of such indicators in the national press is now infamous and there is much anecdotal evidence about the intraorganizational conflict arising from the use of such tables. A questionnaire survey and interview study of clinical directors, clinical service directors and business managers in several Scottish NHS Trusts was undertaken to ascertain the perceptions of local-level managers on the issue of performance indicators. Interviews were also carried out with a number of personnel in the Scottish Office Department of Economics and Information, the Division of Health Gain and the Finance Directorate. This paper explores the differences between the perceptions of the managers at these two levels of the NHS with regards to issues of performance measurement, intraorganizational conflict and corporate vision.

A national appraisal of haemodialysis vascular access provision in Scotland.

PubMed

Oliver, Scott W; Campbell, Jacqueline; Kingsmore, David B; Kasthuri, Ram; Metcalfe, Wendy; Traynor, Jamie P; Fischbacher-Smith, Denis; Jardine, Alan G; Thomson, Peter C

2017-03-21

Published registry data demonstrate longstanding variation in the utilisation of different vascular access (VA) modalities between Scottish renal units; this may reflect different clinical processes between centres. A comprehensive appraisal was undertaken to understand the processes underpinning VA creation and maintenance across Scotland. A mixed methods approach was utilised. Fifty-two semi-structured interviews were conducted with patients and clinicians in all ten, adult and paediatric, Scottish renal units. Interview transcripts were subjected to thematic analysis. Clinical activity data were prospectively collected for six weeks, and correlated with registry data. VA accounts for a large clinical workload. There was significant inter-centre variation in the utilisation of different VA modalities, and patients described frustrating, dissatisfying experiences. VA creation and maintenance pathways functioned best when nephrologists, surgeons and radiologists were co-located on the same campus with close multi-disciplinary working, protected clinical time, and proactive VA maintenance. No unit routinely measured or discussed procedure outcomes or strategic aspects of their service. Varied clinical outcomes reflected varied clinical processes. Optimised clinical pathways, staff education and measurement of clinical outcomes may improve VA service quality and facilitate safer, more effective, patient-centred care.

Proteome-wide Adaptations of Mouse Skeletal Muscles during a Full Month in Space.

PubMed

Tascher, Georg; Brioche, Thomas; Maes, Pauline; Chopard, Angèle; O'Gorman, Donal; Gauquelin-Koch, Guillemette; Blanc, Stéphane; Bertile, Fabrice

2017-07-07

The safety of space flight is challenged by a severe loss of skeletal muscle mass, strength, and endurance that may compromise the health and performance of astronauts. The molecular mechanisms underpinning muscle atrophy and decreased performance have been studied mostly after short duration flights and are still not fully elucidated. By deciphering the muscle proteome changes elicited in mice after a full month aboard the BION-M1 biosatellite, we observed that the antigravity soleus incurred the greatest changes compared with locomotor muscles. Proteomics data notably suggested mitochondrial dysfunction, metabolic and fiber type switching toward glycolytic type II fibers, structural alterations, and calcium signaling-related defects to be the main causes for decreased muscle performance in flown mice. Alterations of the protein balance, mTOR pathway, myogenesis, and apoptosis were expected to contribute to muscle atrophy. Moreover, several signs reflecting alteration of telomere maintenance, oxidative stress, and insulin resistance were found as possible additional deleterious effects. Finally, 8 days of recovery post flight were not sufficient to restore completely flight-induced changes. Thus in-depth proteomics analysis unraveled the complex and multifactorial remodeling of skeletal muscle structure and function during long-term space flight, which should help define combined sets of countermeasures before, during, and after the flight.

Predicting Amyloidogenic Proteins in the Proteomes of Plants.

PubMed

Antonets, Kirill S; Nizhnikov, Anton A

2017-10-16

Amyloids are protein fibrils with characteristic spatial structure. Though amyloids were long perceived to be pathogens that cause dozens of incurable pathologies in humans and mammals, it is currently clear that amyloids also represent a functionally important form of protein structure implicated in a variety of biological processes in organisms ranging from archaea and bacteria to fungi and animals. Despite their social significance, plants remain the most poorly studied group of organisms in the field of amyloid biology. To date, amyloid properties have only been demonstrated in vitro or in heterologous systems for a small number of plant proteins. Here, for the first time, we performed a comprehensive analysis of the distribution of potentially amyloidogenic proteins in the proteomes of approximately 70 species of land plants using the Waltz and SARP (Sequence Analysis based on the Ranking of Probabilities) bioinformatic algorithms. We analyzed more than 2.9 million protein sequences and found that potentially amyloidogenic proteins are abundant in plant proteomes. We found that such proteins are overrepresented among membrane as well as DNA- and RNA-binding proteins of plants. Moreover, seed storage and defense proteins of most plant species are rich in amyloidogenic regions. Taken together, our data demonstrate the diversity of potentially amyloidogenic proteins in plant proteomes and suggest biological processes where formation of amyloids might be functionally important.

The role of internal duplication in the evolution of multi-domain proteins.

PubMed

Nacher, J C; Hayashida, M; Akutsu, T

2010-08-01

Many proteins consist of several structural domains. These multi-domain proteins have likely been generated by selective genome growth dynamics during evolution to perform new functions as well as to create structures that fold on a biologically feasible time scale. Domain units frequently evolved through a variety of genetic shuffling mechanisms. Here we examine the protein domain statistics of more than 1000 organisms including eukaryotic, archaeal and bacterial species. The analysis extends earlier findings on asymmetric statistical laws for proteome to a wider variety of species. While proteins are composed of a wide range of domains, displaying a power-law decay, the computation of domain families for each protein reveals an exponential distribution, characterizing a protein universe composed of a thin number of unique families. Structural studies in proteomics have shown that domain repeats, or internal duplicated domains, represent a small but significant fraction of genome. In spite of its importance, this observation has been largely overlooked until recently. We model the evolutionary dynamics of proteome and demonstrate that these distinct distributions are in fact rooted in an internal duplication mechanism. This process generates the contemporary protein structural domain universe, determines its reduced thickness, and tames its growth. These findings have important implications, ranging from protein interaction network modeling to evolutionary studies based on fundamental mechanisms governing genome expansion.

Structural proteomics: Topology and relative accessibility of plant lipid droplet associated proteins.

PubMed

Jolivet, Pascale; Aymé, Laure; Giuliani, Alexandre; Wien, Frank; Chardot, Thierry; Gohon, Yann

2017-10-03

Lipid droplets are the major stock of lipids in oleaginous plant seeds. Despite their economic importance for oil production and biotechnological issues (biofuels, lubricants and plasticizers), numerous questions about their formation, structure and regulation are still unresolved. To determine water accessible domains of protein coating at lipid droplets surface, a structural proteomic approach has been performed. This technique relies on the millisecond timescale production of hydroxyl radicals by the radiolysis of water using Synchrotron X-ray white beam. Thanks to the evolution of mass spectrometry analysis techniques this approach allows the creation of a map of the solvent accessibility for proteins difficult to study by other means. Using these results, a S3 oleosin water accessibility map is proposed. This is the first time that such a map on an oleosin co-purified with plant lipid droplets and other associated protein is presented. Lipid droplet associated proteins function is linked to stability, structure and probably formation and lipid mobilization of droplets. Structure of these proteins in their native environment, at the interface between bulk water and the lipidic core of these organelles is only based on hydrophobicity plot. Using hydroxyl radical footprinting and proteomics approaches we studied water accessibility of one major protein in these droplets: S3 oleosin of Arabidopsis thaliana seeds. Copyright © 2017 Elsevier B.V. All rights reserved.

Classification and assessment of water bodies as adaptive structural measures for flood risk management planning.

PubMed

McMinn, William R; Yang, Qinli; Scholz, Miklas

2010-09-01

Severe rainfall events have become increasingly common in Europe. Flood defence engineering works are highly capital intensive and can be limited by land availability, leaving land and communities exposed to repeated flooding. Any adaptive drainage structure must have engineered inlets and outlets that control the water level and the rate of release. In Scotland, there are a relatively high number of drinking water reservoirs (operated by Scottish Water), which fall within this defined category and could contribute to flood management control. Reducing the rate of runoff from the upper reaches of a catchment will reduce the volume and peak flows of flood events downstream, thus allowing flood defences to be reduced in size, decreasing the corresponding capital costs. A database of retention basins with flood control potential has been developed for Scotland. The research shows that the majority of small and former drinking water reservoirs are kept full and their spillways are continuously in operation. Utilising some of the available capacity to contribute to flood control could reduce the costs of complying with the EU Flood Directive. Furthermore, the application of a previously developed classification model for Baden in Germany for the Scottish data set showed a lower diversity for basins in Scotland due to less developed infrastructure. The principle value of this approach is a clear and unambiguous categorisation, based on standard variables, which can help to promote communication and understanding between stakeholders. 2010 Elsevier Ltd. All rights reserved.

Selective staining of proteins with hydrophobic surface sites on a native electrophoretic gel.

PubMed

Bertsch, Martina; Kassner, Richard J

2003-01-01

Chemical proteomics aims to characterize all of the proteins in the proteome with respect to their function, which is associated with their interaction with other molecules. We propose the identification of a subproteomic library of expressed proteins whose native structures are typified by the presence of hydrophobic surface sites, which are often involved in interactions with small molecules, membrane lipids, and other proteins, pertaining to their functions. We demonstrate that soluble globular proteins with hydrophobic surface sites can be detected selectively by staining on an electrophoretic gel run under nondenaturing conditions. The application of these staining techniques may help elucidate new catalytic, transport, and regulatory functionalities in complex proteomic screenings.

FINDSITE-metal: Integrating evolutionary information and machine learning for structure-based metal binding site prediction at the proteome level

PubMed Central

Brylinski, Michal; Skolnick, Jeffrey

2010-01-01

The rapid accumulation of gene sequences, many of which are hypothetical proteins with unknown function, has stimulated the development of accurate computational tools for protein function prediction with evolution/structure-based approaches showing considerable promise. In this paper, we present FINDSITE-metal, a new threading-based method designed specifically to detect metal binding sites in modeled protein structures. Comprehensive benchmarks using different quality protein structures show that weakly homologous protein models provide sufficient structural information for quite accurate annotation by FINDSITE-metal. Combining structure/evolutionary information with machine learning results in highly accurate metal binding annotations; for protein models constructed by TASSER, whose average Cα RMSD from the native structure is 8.9 Å, 59.5% (71.9%) of the best of top five predicted metal locations are within 4 Å (8 Å) from a bound metal in the crystal structure. For most of the targets, multiple metal binding sites are detected with the best predicted binding site at rank 1 and within the top 2 ranks in 65.6% and 83.1% of the cases, respectively. Furthermore, for iron, copper, zinc, calcium and magnesium ions, the binding metal can be predicted with high, typically 70-90%, accuracy. FINDSITE-metal also provides a set of confidence indexes that help assess the reliability of predictions. Finally, we describe the proteome-wide application of FINDSITE-metal that quantifies the metal binding complement of the human proteome. FINDSITE-metal is freely available to the academic community at http://cssb.biology.gatech.edu/findsite-metal/. PMID:21287609

Skeletal muscle proteomic signature and metabolic impairment in pulmonary hypertension.

PubMed

Malenfant, Simon; Potus, François; Fournier, Frédéric; Breuils-Bonnet, Sandra; Pflieger, Aude; Bourassa, Sylvie; Tremblay, Ève; Nehmé, Benjamin; Droit, Arnaud; Bonnet, Sébastien; Provencher, Steeve

2015-05-01

Exercise limitation comes from a close interaction between cardiovascular and skeletal muscle impairments. To better understand the implication of possible peripheral oxidative metabolism dysfunction, we studied the proteomic signature of skeletal muscle in pulmonary arterial hypertension (PAH). Eight idiopathic PAH patients and eight matched healthy sedentary subjects were evaluated for exercise capacity, skeletal muscle proteomic profile, metabolism, and mitochondrial function. Skeletal muscle proteins were extracted, and fractioned peptides were tagged using an iTRAQ protocol. Proteomic analyses have documented a total of 9 downregulated proteins in PAH skeletal muscles and 10 upregulated proteins compared to healthy subjects. Most of the downregulated proteins were related to mitochondrial structure and function. Focusing on skeletal muscle metabolism and mitochondrial health, PAH patients presented a decreased expression of oxidative enzymes (pyruvate dehydrogenase, p < 0.01) and an increased expression of glycolytic enzymes (lactate dehydrogenase activity, p < 0.05). These findings were supported by abnormal mitochondrial morphology on electronic microscopy, lower citrate synthase activity (p < 0.01) and lower expression of the transcription factor A of the mitochondria (p < 0.05), confirming a more glycolytic metabolism in PAH skeletal muscles. We provide evidences that impaired mitochondrial and metabolic functions found in the lungs and the right ventricle are also present in skeletal muscles of patients. • Proteomic and metabolic analysis show abnormal oxidative metabolism in PAH skeletal muscle. • EM of PAH patients reveals abnormal mitochondrial structure and distribution. • Abnormal mitochondrial health and function contribute to exercise impairments of PAH. • PAH may be considered a vascular affliction of heart and lungs with major impact on peripheral muscles.

Early examples of art in Scottish hospitals, 2: Crichton Royal Hospital, Dumfries.

PubMed

Park, Maureen

2003-12-01

Fine art has been used in hospitals for centuries. However, Crichton Royal Hospital in Dumfries pioneered the use of art activity in the treatment of its patients. This article is the second of two which look at examples of art created for, and in, Scottish hospitals in the 19th century. It is suggested that the importance of Scotland's contribution to this movement is unrecognized by many of its modern-day practitioners.

The relationship between waiting times and 'adherence' to the Scottish Intercollegiate Guidelines Network 98 guideline in autism spectrum disorder diagnostic services in Scotland.

PubMed

McKenzie, Karen; Forsyth, Kirsty; O'Hare, Anne; McClure, Iain; Rutherford, Marion; Murray, Aja; Irvine, Linda

2016-05-01

The aim of this study was to explore the extent to which the Scottish Intercollegiate Guidelines Network 98 guidelines on the assessment and diagnosis of autism spectrum disorder were adhered to in child autism spectrum disorder diagnostic services in Scotland and whether there was a significant relationship between routine practice which more closely reflected these recommendations (increased adherence) and increased waiting times. Retrospective, cross-sectional case note analysis was applied to data from 80 case notes. Adherence ranged from a possible 0 (no adherence) to 19 (full adherence). Overall, 17/22 of the recommendations were adhered to in over 50 of the 80 cases and in 70 or more cases for 11/22 of the recommendations, with a mean adherence score of 16 (standard deviation = 1.9). No significant correlation was found between adherence and total wait time for untransformed (r = 0.15, p = 0.32) or transformed data (r = 0.12, p = 0.20). The results indicated that the assessment and diagnostic practices were consistent with the relevant Scottish Intercollegiate Guidelines Network 98 guideline recommendations. Increased adherence to the 19 included recommendations was not significantly related to increased total waiting times, indicating that the Scottish Intercollegiate Guidelines Network 98 recommendations have generally been integrated into practice, without a resultant increase in patient waits. © The Author(s) 2015.

A study of the CCG polymorphism in the IT15 cDNA in the Scottish Huntington`s disease and normal populations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barron, L.H.; Rae, A.; Brock, D.J.H.

1994-09-01

The CCG rich sequence immediately 3{prime} to the CAG repeat that is expanded in Huntington`s disease (HD) has recently been shown to be polymorphic with at least 5 alleles differing by multiples of 3 bp being found in the normal population. We have studied the allele distribution in 200 Scottish HD families and have found very strong evidence for almost complete disequilibrium in this population. For all the families phase was unambiguously determined and 196 were shown to have a CCG repeat allele of 176 bp cosegregating with the HD chromosome. This observation is significantly different to the normal populationmore » distribution where 31% of people have an allele of 185 bp. This overrepresentation of the 176 bp allele is also seen in the normal population on chromosomes with greater than 26 CAG repeats. The DNA sequence across the CAG and CCG repeats has been obtained for the four HD patients that do not have a 176 bp CCG repeat size and will be presented. We present strong evidence of genetic heterogeneity in the Scottish HD population making it very unlikely that there is a founder effect in the Scottish HD population. These data suggest that we may have identified a region of the IT15 gene that is critical in the mechanism of Huntington`s disease CAG expansion.« less

Public Health and Unconventional Oil and Gas Extraction Including Fracking: Global Lessons from a Scottish Government Review.

PubMed

Watterson, Andrew; Dinan, William

2018-04-04

Unconventional oil and gas extraction (UOGE) including fracking for shale gas is underway in North America on a large scale, and in Australia and some other countries. It is viewed as a major source of global energy needs by proponents. Critics consider fracking and UOGE an immediate and long-term threat to global, national, and regional public health and climate. Rarely have governments brought together relatively detailed assessments of direct and indirect public health risks associated with fracking and weighed these against potential benefits to inform a national debate on whether to pursue this energy route. The Scottish government has now done so in a wide-ranging consultation underpinned by a variety of reports on unconventional gas extraction including fracking. This paper analyses the Scottish government approach from inception to conclusion, and from procedures to outcomes. The reports commissioned by the Scottish government include a comprehensive review dedicated specifically to public health as well as reports on climate change, economic impacts, transport, geology, and decommissioning. All these reports are relevant to public health, and taken together offer a comprehensive review of existing evidence. The approach is unique globally when compared with UOGE assessments conducted in the USA, Australia, Canada, and England. The review process builds a useful evidence base although it is not without flaws. The process approach, if not the content, offers a framework that may have merits globally.

A phylogenomic data-driven exploration of viral origins and evolution

PubMed Central

Nasir, Arshan; Caetano-Anollés, Gustavo

2015-01-01

The origin of viruses remains mysterious because of their diverse and patchy molecular and functional makeup. Although numerous hypotheses have attempted to explain viral origins, none is backed by substantive data. We take full advantage of the wealth of available protein structural and functional data to explore the evolution of the proteomic makeup of thousands of cells and viruses. Despite the extremely reduced nature of viral proteomes, we established an ancient origin of the “viral supergroup” and the existence of widespread episodes of horizontal transfer of genetic information. Viruses harboring different replicon types and infecting distantly related hosts shared many metabolic and informational protein structural domains of ancient origin that were also widespread in cellular proteomes. Phylogenomic analysis uncovered a universal tree of life and revealed that modern viruses reduced from multiple ancient cells that harbored segmented RNA genomes and coexisted with the ancestors of modern cells. The model for the origin and evolution of viruses and cells is backed by strong genomic and structural evidence and can be reconciled with existing models of viral evolution if one considers viruses to have originated from ancient cells and not from modern counterparts. PMID:26601271

The Escherichia coli Peripheral Inner Membrane Proteome*

PubMed Central

Papanastasiou, Malvina; Orfanoudaki, Georgia; Koukaki, Marina; Kountourakis, Nikos; Sardis, Marios Frantzeskos; Aivaliotis, Michalis; Karamanou, Spyridoula; Economou, Anastassios

2013-01-01

Biological membranes are essential for cell viability. Their functional characteristics strongly depend on their protein content, which consists of transmembrane (integral) and peripherally associated membrane proteins. Both integral and peripheral inner membrane proteins mediate a plethora of biological processes. Whereas transmembrane proteins have characteristic hydrophobic stretches and can be predicted using bioinformatics approaches, peripheral inner membrane proteins are hydrophilic, exist in equilibria with soluble pools, and carry no discernible membrane targeting signals. We experimentally determined the cytoplasmic peripheral inner membrane proteome of the model organism Escherichia coli using a multidisciplinary approach. Initially, we extensively re-annotated the theoretical proteome regarding subcellular localization using literature searches, manual curation, and multi-combinatorial bioinformatics searches of the available databases. Next we used sequential biochemical fractionations coupled to direct identification of individual proteins and protein complexes using high resolution mass spectrometry. We determined that the proposed cytoplasmic peripheral inner membrane proteome occupies a previously unsuspected ∼19% of the basic E. coli BL21(DE3) proteome, and the detected peripheral inner membrane proteome occupies ∼25% of the estimated expressed proteome of this cell grown in LB medium to mid-log phase. This value might increase when fleeting interactions, not studied here, are taken into account. Several proteins previously regarded as exclusively cytoplasmic bind membranes avidly. Many of these proteins are organized in functional or/and structural oligomeric complexes that bind to the membrane with multiple interactions. Identified proteins cover the full spectrum of biological activities, and more than half of them are essential. Our data suggest that the cytoplasmic proteome displays remarkably dynamic and extensive communication with biological membrane surfaces that we are only beginning to decipher. PMID:23230279

'Out of two bad choices, I took the slightly better one': vaccination dilemmas for Scottish and Polish migrant women during the H1N1 influenza pandemic.

PubMed

Sim, J A; Ulanika, A A; Katikireddi, S V; Gorman, D

2011-08-01

Pregnancy has been identified as a risk factor for complications from pandemic H1N1 influenza, and pregnant women were identified as a target group for vaccination in the UK in the 2009 pandemic. Poland took a more conservative approach, and did not offer vaccination to pregnant women. Poland accounts for the largest wave of recent migrants to the UK, many of whom are in their reproductive years and continue to participate actively in Polish healthcare systems after migration. The authors speculated that different national responses may shape differences in approaches to the vaccine between Scottish and Polish women. This study therefore aimed to assess how pregnant Polish migrants to Scotland weighed up the risks and benefits of the vaccine for pandemic H1N1 influenza in comparison with their Scottish counterparts. A qualitative interview-based study comparing the views of Scottish and Polish pregnant women on H1N1 vaccination was carried out in 'real time' during the first 2 weeks of the vaccination programme in November 2009. One-to-one interviews were conducted with 10 women (five Polish and five Scottish) in their native language. Interviews were transcribed, translated, coded and analysed for differences and similarities in decision-making processes between the two groups. Contrary to expectations, Scottish and Polish women drew on a strikingly similar set of considerations in deciding whether or not to accept the vaccine, with individual women reaching different conclusions. Almost all of the women adopted a critical stance towards the vaccine. While most women understood that pregnancy was a risk factor for complications from influenza, their primary concern was protecting family health overall and their fetus in particular. Deciding whether or not to accept the vaccine was difficult for women. Some identified a contradiction between the culture of caution which characterizes pregnancy-related advice, and the fact that they were being urged to accept what was perceived as a relatively untested vaccine. Their health histories, individual constitutions, and whether their everyday routines exposed them to sources of infection combined to establish their perceived 'candidacy' for contracting infection. Neither Scottish nor Polish women felt that 'official' information addressed their concerns in sufficient detail, and almost all of the women sought information from a variety of sources. Polish women found it more difficult to access information and advice from the National Health Service than their Scottish counterparts. For most respondents, deciding whether or not to accept the vaccine was an attenuated process, culminating for many in choosing the 'least worst' option in the context of competing risks. To the authors' knowledge, this is the first study to assess perceptions of H1N1 immunization risk in pregnant women in 'real time'. It highlights the important unmet needs for information that women need to be able to make informed vaccination choices, and the challenges of producing such information in a context of uncertainty. This is of particular relevance as many countries, including the UK, are actively reviewing their plans for vaccination programmes during pregnancy. Copyright © 2011 The Royal Society for Public Health. Published by Elsevier Ltd. All rights reserved.

Mortality, ethnicity, and country of birth on a national scale, 2001-2013: A retrospective cohort (Scottish Health and Ethnicity Linkage Study).

PubMed

Bhopal, Raj S; Gruer, Laurence; Cezard, Genevieve; Douglas, Anne; Steiner, Markus F C; Millard, Andrew; Buchanan, Duncan; Katikireddi, S Vittal; Sheikh, Aziz

2018-03-01

Migrant and ethnic minority groups are often assumed to have poor health relative to the majority population. Few countries have the capacity to study a key indicator, mortality, by ethnicity and country of birth. We hypothesized at least 10% differences in mortality by ethnic group in Scotland that would not be wholly attenuated by adjustment for socio-economic factors or country of birth. We linked the Scottish 2001 Census to mortality data (2001-2013) in 4.62 million people (91% of estimated population), calculating age-adjusted mortality rate ratios (RRs; multiplied by 100 as percentages) with 95% confidence intervals (CIs) for 13 ethnic groups, with the White Scottish group as reference (ethnic group classification follows the Scottish 2001 Census). The Scottish Index of Multiple Deprivation, education status, and household tenure were socio-economic status (SES) confounding variables and born in the UK or Republic of Ireland (UK/RoI) an interacting and confounding variable. Smoking and diabetes data were from a primary care sub-sample (about 53,000 people). Males and females in most minority groups had lower age-adjusted mortality RRs than the White Scottish group. The 95% CIs provided good evidence that the RR was more than 10% lower in the following ethnic groups: Other White British (72.3 [95% CI 64.2, 81.3] in males and 75.2 [68.0, 83.2] in females); Other White (80.8 [72.8, 89.8] in males and 76.2 [68.6, 84.7] in females); Indian (62.6 [51.6, 76.0] in males and 60.7 [50.4, 73.1] in females); Pakistani (66.1 [57.4, 76.2] in males and 73.8 [63.7, 85.5] in females); Bangladeshi males (50.7 [32.5, 79.1]); Caribbean females (57.5 [38.5, 85.9]); and Chinese (52.2 [43.7, 62.5] in males and 65.8 [55.3, 78.2] in females). The differences were diminished but not eliminated after adjusting for UK/RoI birth and SES variables. A mortality advantage was evident in all 12 minority groups for those born abroad, but in only 6/12 male groups and 5/12 female groups of those born in the UK/RoI. In the primary care sub-sample, after adjustment for age, UK/RoI born, SES, smoking, and diabetes, the RR was not lower in Indian males (114.7 [95% CI 78.3, 167.9]) and Pakistani females (103.9 [73.9, 145.9]) than in White Scottish males and females, respectively. The main limitations were the inability to include deaths abroad and the small number of deaths in some ethnic minority groups, especially for people born in the UK/RoI. There was relatively low mortality for many ethnic minority groups compared to the White Scottish majority. The mortality advantage was less clear in UK/RoI-born minority group offspring than in immigrants. These differences need explaining, and health-related behaviours seem important. Similar analyses are required internationally to fulfil agreed goals for monitoring, understanding, and improving health in ethnically diverse societies and to apply to health policy, especially on health inequalities and inequities.

Nose profile morphology and accuracy study of nose profile estimation method in Scottish subadult and Indonesian adult populations.

PubMed

Sarilita, Erli; Rynn, Christopher; Mossey, Peter A; Black, Sue; Oscandar, Fahmi

2018-05-01

This study investigated nose profile morphology and its relationship to the skull in Scottish subadult and Indonesian adult populations, with the aim of improving the accuracy of forensic craniofacial reconstruction. Samples of 86 lateral head cephalograms from Dundee Dental School (mean age, 11.8 years) and 335 lateral head cephalograms from the Universitas Padjadjaran Dental Hospital, Bandung, Indonesia (mean age 24.2 years), were measured. The method of nose profile estimation based on skull morphology previously proposed by Rynn and colleagues in 2010 (FSMP 6:20-34) was tested in this study. Following this method, three nasal aperture-related craniometrics and six nose profile dimensions were measured from the cephalograms. To assess the accuracy of the method, six nose profile dimensions were estimated from the three craniometric parameters using the published method and then compared to the actual nose profile dimensions.In the Scottish subadult population, no sexual dimorphism was evident in the measured dimensions. In contrast, sexual dimorphism of the Indonesian adult population was evident in all craniometric and nose profile dimensions; notably, males exhibited statistically significant larger values than females. The published method by Rynn and colleagues (FSMP 6:20-34, 2010) performed better in the Scottish subadult population (mean difference of maximum, 2.35 mm) compared to the Indonesian adult population (mean difference of maximum, 5.42 mm in males and 4.89 mm in females).In addition, regression formulae were derived to estimate nose profile dimensions based on the craniometric measurements for the Indonesian adult population. The published method is not sufficiently accurate for use on the Indonesian population, so the derived method should be used. The accuracy of the published method by Rynn and colleagues (FSMP 6:20-34, 2010) was sufficiently reliable to be applied in Scottish subadult population.

Scottish adolescents' sun-related behaviours, tanning attitudes and associations with skin cancer awareness: a cross-sectional study.

PubMed

Kyle, Richard G; Macmillan, Iona; Forbat, Liz; Neal, Richard D; O'Carroll, Ronan E; Haw, Sally; Hubbard, Gill

2014-05-02

To describe Scottish adolescents' sun-related behaviours and tanning attitudes and assess associations with skin cancer awareness. Cross-sectional study. 20 state secondary schools in one Scottish local authority (Glasgow City). 2173 adolescents (females: 50.7%, n=1102) with a mean age of 12.4 (SD=0.55). Sun-related behaviour (suntan, sunbathing, sunburn, sunscreen use, sunbed use), tanning attitudes, skin cancer-related symptom and risk factor awareness. Adolescents reported poor sun-related practice: 51% of adolescents reported sunburn the previous summer of whom 38% indicated sunburn on more than one occasion. Skin cancer awareness was low: 45% recognised 'change in the appearance of a mole' as a cancer symptom, and 39% agreed that 'getting sunburnt more than once as a child' increased cancer risk. 42% and 26% of adolescents, respectively, reported that friends and family held protanning attitudes. Compared with males, females were statistically significantly more likely to: report sunbathing (p<0.001), use of lotions or oil to aid tanning (p=0.009) and sunburn (p<0.001); know that changes in the appearance of a mole was a skin cancer symptom (p=0.036) and sunburn more than once as a child was a skin cancer risk factor (p=0.005); perceive their friends to hold protanning attitudes (p<0.001) and indicate that a tan made them feel better about themselves (p<0.001), more attractive to others (p=0.011) and healthier (p<0.001). Scottish adolescents had poor sun protection practice and low skin cancer awareness. Girls adopted riskier sun-related behaviour despite greater awareness of skin cancer-related risk. Urgent action is required to promote positive sun-related behaviour and increase skin cancer awareness among Scottish adolescents. However, further research is needed to inform the development of effective sun-safe interventions.

Scottish adolescents’ sun-related behaviours, tanning attitudes and associations with skin cancer awareness: a cross-sectional study

PubMed Central

Kyle, Richard G; MacMillan, Iona; Forbat, Liz; Neal, Richard D; O'Carroll, Ronan E; Haw, Sally; Hubbard, Gill

2014-01-01

Objectives To describe Scottish adolescents’ sun-related behaviours and tanning attitudes and assess associations with skin cancer awareness. Design Cross-sectional study. Setting 20 state secondary schools in one Scottish local authority (Glasgow City). Participants 2173 adolescents (females: 50.7%, n=1102) with a mean age of 12.4 (SD=0.55). Outcome measures Sun-related behaviour (suntan, sunbathing, sunburn, sunscreen use, sunbed use), tanning attitudes, skin cancer-related symptom and risk factor awareness. Results Adolescents reported poor sun-related practice: 51% of adolescents reported sunburn the previous summer of whom 38% indicated sunburn on more than one occasion. Skin cancer awareness was low: 45% recognised ‘change in the appearance of a mole’ as a cancer symptom, and 39% agreed that ‘getting sunburnt more than once as a child’ increased cancer risk. 42% and 26% of adolescents, respectively, reported that friends and family held protanning attitudes. Compared with males, females were statistically significantly more likely to: report sunbathing (p<0.001), use of lotions or oil to aid tanning (p=0.009) and sunburn (p<0.001); know that changes in the appearance of a mole was a skin cancer symptom (p=0.036) and sunburn more than once as a child was a skin cancer risk factor (p=0.005); perceive their friends to hold protanning attitudes (p<0.001) and indicate that a tan made them feel better about themselves (p<0.001), more attractive to others (p=0.011) and healthier (p<0.001). Conclusions Scottish adolescents had poor sun protection practice and low skin cancer awareness. Girls adopted riskier sun-related behaviour despite greater awareness of skin cancer-related risk. Urgent action is required to promote positive sun-related behaviour and increase skin cancer awareness among Scottish adolescents. However, further research is needed to inform the development of effective sun-safe interventions. PMID:24793258

Facile preparation of salivary extracellular vesicles for cancer proteomics

NASA Astrophysics Data System (ADS)

Sun, Yan; Xia, Zhijun; Shang, Zhi; Sun, Kaibo; Niu, Xiaomin; Qian, Liqiang; Fan, Liu-Yin; Cao, Cheng-Xi; Xiao, Hua

2016-04-01

Extracellular vesicles (EVs) are membrane surrounded structures released by cells, which have been increasingly recognized as mediators of intercellular communication. Recent reports indicate that EVs participate in important biological processes and could serve as potential source for cancer biomarkers. As an attractive EVs source with merit of non-invasiveness, human saliva is a unique medium for clinical diagnostics. Thus, we proposed a facile approach to prepare salivary extracellular vesicles (SEVs). Affinity chromatography column combined with filter system (ACCF) was developed to efficiently remove the high abundant proteins and viscous interferences of saliva. Protein profiling in the SEVs obtained by this strategy was compared with conventional centrifugation method, which demonstrated that about 70% more SEVs proteins could be revealed. To explore its utility for cancer proteomics, we analyzed the proteome of SEVs in lung cancer patients and normal controls. Shotgun proteomic analysis illustrated that 113 and 95 proteins have been identified in cancer group and control group, respectively. Among those 63 proteins that have been consistently discovered only in cancer group, 12 proteins are lung cancer related. Our results demonstrated that SEVs prepared through the developed strategy are valuable samples for proteomics and could serve as a promising liquid biopsy for cancer.

Unraveling the resistance of microbial biofilms: has proteomics been helpful?

PubMed

Seneviratne, C Jayampath; Wang, Yu; Jin, Lijian; Wong, Sarah S W; Herath, Thanuja D K; Samaranayake, Lakshman P

2012-02-01

Biofilms are surface-attached, matrix-encased, structured microbial communities which display phenotypic features that are dramatically different from those of their free-floating, or planktonic, counterparts. Biofilms seem to be the preferred mode of growth of microorganisms in nature, and at least 65% of all human infections are associated with biofilms. The most notable and clinically relevant property of biofilms is their greater resistance to antimicrobials compared with their planktonic counterparts. Although both bacterial and fungal biofilms display this phenotypic feature, the exact mechanisms underlying their increased drug resistance are yet to be determined. Advances in proteomics techniques during the past decade have facilitated in-depth analysis of the possible mechanisms underpinning increased drug resistance in biofilms. These studies have demonstrated the ability of proteomics techniques to unravel new targets for combating microbial biofilms. In this review, we discuss the putative drug resistance mechanisms of microbial biofilms that have been uncovered by proteomics and critically evaluate the possible contribution of the new knowledge to future development in the field. We also summarize strategic uses of novel proteomics technologies in studies related to drug resistance mechanisms of microbial biofilms. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Boosting the globalization of plant proteomics through INPPO: current developments and future prospects.

PubMed

Agrawal, Ganesh Kumar; Sarkar, Abhijit; Agrawal, Raj; Ndimba, Bongani Kaiser; Tanou, Georgia; Dunn, Michael J; Kieselbach, Thomas; Cramer, Rainer; Wienkoop, Stefanie; Chen, Sixue; Rafudeen, Mohammed Suhail; Deswal, Renu; Barkla, Bronwyn J; Weckwerth, Wolfram; Heazlewood, Joshua L; Renaut, Jenny; Job, Dominique; Chakraborty, Niranjan; Rakwal, Randeep

2012-02-01

The International Plant Proteomics Organization (INPPO) is a non-profit-organization consisting of people who are involved or interested in plant proteomics. INPPO is constantly growing in volume and activity, which is mostly due to the realization among plant proteomics researchers worldwide for the need of such a global platform. Their active participation resulted in the rapid growth within the first year of INPPO's official launch in 2011 via its website (www.inppo.com) and publication of the 'Viewpoint paper' in a special issue of PROTEOMICS (May 2011). Here, we will be highlighting the progress achieved in the year 2011 and the future targets for the year 2012 and onwards. INPPO has achieved a successful administrative structure, the Core Committee (CC; composed of President, Vice-President, and General Secretaries), Executive Council (EC), and General Body (GB) to achieve INPPO objectives. Various committees and subcommittees are in the process of being functionalized via discussion amongst scientists around the globe. INPPO's primary aim to popularize the plant proteomics research in biological sciences has also been recognized by PROTEOMICS where a section dedicated to plant proteomics has been introduced starting January 2012, following the very first issue of this journal devoted to plant proteomics in May 2011. To disseminate organizational activities to the scientific community, INPPO has launched a biannual (in January and July) newsletter entitled 'INPPO Express: News & Views' with the first issue published in January 2012. INPPO is also planning to have several activities in 2012, including programs within the Education Outreach committee in different countries, and the development of research ideas and proposals with priority on crop and horticultural plants, while keeping tight interactions with proteomics programs on model plants such as Arabidopsis thaliana, rice, and Medicago truncatula. Altogether, the INPPO progress and upcoming activities are because of immense support, dedication, and hard work of all members of the INPPO community, and also due to the wide encouragement and support from the communities (scientific and non-scientific). Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Correlating low-similarity peptide sequences and allergenic epitopes.

PubMed

Kanduc, D

2008-01-01

Although a high number of allergenic peptide epitopes has been experimentally identified and defined, the molecular basis and the precise mechanisms underlying peptide allergenicity are unknown. This issue was analyzed exploring the relationship between peptide allergenicity and sequence similarity to the human proteome. The structured analysis of the data reported in literature put into evidence that the most part of IgE-binding epitopes are (or harbor) pentapeptide unit(s) with no/low similarity to the human proteome, this way suggesting that no or low sequence similarity to the host proteome might represent a minimum common denominator identifying allergenic peptides. The present literature analysis might be of relevance in devising and designing short amino acid modules to be used for blocking pathogenic IgE.

The Lipid Raft Proteome of African Trypanosomes Contains Many Flagellar Proteins.

PubMed

Sharma, Aabha I; Olson, Cheryl L; Engman, David M

2017-08-24

Lipid rafts are liquid-ordered membrane microdomains that form by preferential association of 3-β-hydroxysterols, sphingolipids and raft-associated proteins often having acyl modifications. We isolated lipid rafts of the protozoan parasite Trypanosoma brucei and determined the protein composition of lipid rafts in the cell. This analysis revealed a striking enrichment of flagellar proteins and several putative signaling proteins in the lipid raft proteome. Calpains and intraflagellar transport proteins, in particular, were found to be abundant in the lipid raft proteome. These findings provide additional evidence supporting the notion that the eukaryotic cilium/flagellum is a lipid raft-enriched specialized structure with high concentrations of sterols, sphingolipids and palmitoylated proteins involved in environmental sensing and cell signaling.

The Lipid Raft Proteome of African Trypanosomes Contains Many Flagellar Proteins

PubMed Central

Sharma, Aabha I.; Olson, Cheryl L.; Engman, David M.

2017-01-01

Lipid rafts are liquid-ordered membrane microdomains that form by preferential association of 3-β-hydroxysterols, sphingolipids and raft-associated proteins often having acyl modifications. We isolated lipid rafts of the protozoan parasite Trypanosoma brucei and determined the protein composition of lipid rafts in the cell. This analysis revealed a striking enrichment of flagellar proteins and several putative signaling proteins in the lipid raft proteome. Calpains and intraflagellar transport proteins, in particular, were found to be abundant in the lipid raft proteome. These findings provide additional evidence supporting the notion that the eukaryotic cilium/flagellum is a lipid raft-enriched specialized structure with high concentrations of sterols, sphingolipids and palmitoylated proteins involved in environmental sensing and cell signaling. PMID:28837104

Active site specificity profiling datasets of matrix metalloproteinases (MMPs) 1, 2, 3, 7, 8, 9, 12, 13 and 14.

PubMed

Eckhard, Ulrich; Huesgen, Pitter F; Schilling, Oliver; Bellac, Caroline L; Butler, Georgina S; Cox, Jennifer H; Dufour, Antoine; Goebeler, Verena; Kappelhoff, Reinhild; Auf dem Keller, Ulrich; Klein, Theo; Lange, Philipp F; Marino, Giada; Morrison, Charlotte J; Prudova, Anna; Rodriguez, David; Starr, Amanda E; Wang, Yili; Overall, Christopher M

2016-06-01

The data described provide a comprehensive resource for the family-wide active site specificity portrayal of the human matrix metalloproteinase family. We used the high-throughput proteomic technique PICS (Proteomic Identification of protease Cleavage Sites) to comprehensively assay 9 different MMPs. We identified more than 4300 peptide cleavage sites, spanning both the prime and non-prime sides of the scissile peptide bond allowing detailed subsite cooperativity analysis. The proteomic cleavage data were expanded by kinetic analysis using a set of 6 quenched-fluorescent peptide substrates designed using these results. These datasets represent one of the largest specificity profiling efforts with subsequent structural follow up for any protease family and put the spotlight on the specificity similarities and differences of the MMP family. A detailed analysis of this data may be found in Eckhard et al. (2015) [1]. The raw mass spectrometry data and the corresponding metadata have been deposited in PRIDE/ProteomeXchange with the accession number PXD002265.

Proteomic changes involved in tenderization of bovine Longissimus dorsi muscle during prolonged ageing.

PubMed

Polati, Rita; Menini, Michele; Robotti, Elisa; Millioni, Renato; Marengo, Emilio; Novelli, Enrico; Balzan, Stefania; Cecconi, Daniela

2012-12-01

To study proteomic changes involved in tenderization of bovine Longissimus dorsi four Charolaise heifers and four Charolaise bull's muscles were sampled at slaughter after early and long ageing (2-4°C for 12 and 26days respectively). Descriptive sensory evaluation of samples were performed and their tenderness evaluated by Warner-Bratzler shear force test. Protein composition of fresh muscle and of meat aged was analysed by cartesian and polar 2-D electrophoresis. Student's t-test and Ranking-PCA analyses were performed to detect proteomic modulation, and the selected protein spots were identified by nano-HPLC-Chip MS/MS. This research has demonstrated that there are no differences between proteomic patterns of male and females Longissimus dorsi muscle, and that the extension of ageing beyond 12days, did not brings any concrete advantage in terms of sensory quality. Furthermore, the data presented here demonstrated that meat maturation caused changes of the abundance of proteins involved in metabolic, structural, and stress related processes. Copyright © 2012 Elsevier Ltd. All rights reserved.

Mass spectrometry-based proteomics: basic principles and emerging technologies and directions.

PubMed

Van Riper, Susan K; de Jong, Ebbing P; Carlis, John V; Griffin, Timothy J

2013-01-01

As the main catalytic and structural molecules within living systems, proteins are the most likely biomolecules to be affected by radiation exposure. Proteomics, the comprehensive characterization of proteins within complex biological samples, is therefore a research approach ideally suited to assess the effects of radiation exposure on cells and tissues. For comprehensive characterization of proteomes, an analytical platform capable of quantifying protein abundance, identifying post-translation modifications and revealing members of protein complexes on a system-wide level is necessary. Mass spectrometry (MS), coupled with technologies for sample fractionation and automated data analysis, provides such a versatile and powerful platform. In this chapter we offer a view on the current state of MS-proteomics, and focus on emerging technologies within three areas: (1) New instrumental methods; (2) New computational methods for peptide identification; and (3) Label-free quantification. These emerging technologies should be valuable for researchers seeking to better understand biological effects of radiation on living systems.

Role of the visual experience-dependent nascent proteome in neuronal plasticity

PubMed Central

Liu, Han-Hsuan; McClatchy, Daniel B; Schiapparelli, Lucio; Shen, Wanhua; Yates, John R

2018-01-01

Experience-dependent synaptic plasticity refines brain circuits during development. To identify novel protein synthesis-dependent mechanisms contributing to experience-dependent plasticity, we conducted a quantitative proteomic screen of the nascent proteome in response to visual experience in Xenopus optic tectum using bio-orthogonal metabolic labeling (BONCAT). We identified 83 differentially synthesized candidate plasticity proteins (CPPs). The CPPs form strongly interconnected networks and are annotated to a variety of biological functions, including RNA splicing, protein translation, and chromatin remodeling. Functional analysis of select CPPs revealed the requirement for eukaryotic initiation factor three subunit A (eIF3A), fused in sarcoma (FUS), and ribosomal protein s17 (RPS17) in experience-dependent structural plasticity in tectal neurons and behavioral plasticity in tadpoles. These results demonstrate that the nascent proteome is dynamic in response to visual experience and that de novo synthesis of machinery that regulates RNA splicing and protein translation is required for experience-dependent plasticity. PMID:29412139

Understanding the development of minimum unit pricing of alcohol in Scotland: a qualitative study of the policy process.

PubMed

Katikireddi, Srinivasa Vittal; Hilton, Shona; Bonell, Chris; Bond, Lyndal

2014-01-01

Minimum unit pricing of alcohol is a novel public health policy with the potential to improve population health and reduce health inequalities. Theories of the policy process may help to understand the development of policy innovation and in turn identify lessons for future public health research and practice. This study aims to explain minimum unit pricing's development by taking a 'multiple-lenses' approach to understanding the policy process. In particular, we apply three perspectives of the policy process (Kingdon's multiple streams, Punctuated-Equilibrium Theory, Multi-Level Governance) to understand how and why minimum unit pricing has developed in Scotland and describe implications for efforts to develop evidence-informed policymaking. Semi-structured interviews were conducted with policy actors (politicians, civil servants, academics, advocates, industry representatives) involved in the development of MUP (n = 36). Interviewees were asked about the policy process and the role of evidence in policy development. Data from two other sources (a review of policy documents and an analysis of evidence submission documents to the Scottish Parliament) were used for triangulation. The three perspectives provide complementary understandings of the policy process. Evidence has played an important role in presenting the policy issue of alcohol as a problem requiring action. Scotland-specific data and a change in the policy 'image' to a population-based problem contributed to making alcohol-related harms a priority for action. The limited powers of Scottish Government help explain the type of price intervention pursued while distinct aspects of the Scottish political climate favoured the pursuit of price-based interventions. Evidence has played a crucial but complex role in the development of an innovative policy. Utilising different political science theories helps explain different aspects of the policy process, with Multi-Level Governance particularly useful for highlighting important lessons for the future of public health policy.

Understanding the Development of Minimum Unit Pricing of Alcohol in Scotland: A Qualitative Study of the Policy Process

PubMed Central

Katikireddi, Srinivasa Vittal; Hilton, Shona; Bonell, Chris; Bond, Lyndal

2014-01-01

Background Minimum unit pricing of alcohol is a novel public health policy with the potential to improve population health and reduce health inequalities. Theories of the policy process may help to understand the development of policy innovation and in turn identify lessons for future public health research and practice. This study aims to explain minimum unit pricing’s development by taking a ‘multiple-lenses’ approach to understanding the policy process. In particular, we apply three perspectives of the policy process (Kingdon’s multiple streams, Punctuated-Equilibrium Theory, Multi-Level Governance) to understand how and why minimum unit pricing has developed in Scotland and describe implications for efforts to develop evidence-informed policymaking. Methods Semi-structured interviews were conducted with policy actors (politicians, civil servants, academics, advocates, industry representatives) involved in the development of MUP (n = 36). Interviewees were asked about the policy process and the role of evidence in policy development. Data from two other sources (a review of policy documents and an analysis of evidence submission documents to the Scottish Parliament) were used for triangulation. Findings The three perspectives provide complementary understandings of the policy process. Evidence has played an important role in presenting the policy issue of alcohol as a problem requiring action. Scotland-specific data and a change in the policy ‘image’ to a population-based problem contributed to making alcohol-related harms a priority for action. The limited powers of Scottish Government help explain the type of price intervention pursued while distinct aspects of the Scottish political climate favoured the pursuit of price-based interventions. Conclusions Evidence has played a crucial but complex role in the development of an innovative policy. Utilising different political science theories helps explain different aspects of the policy process, with Multi-Level Governance particularly useful for highlighting important lessons for the future of public health policy. PMID:24670519

Do Viruses Exchange Genes across Superkingdoms of Life?

PubMed

Malik, Shahana S; Azem-E-Zahra, Syeda; Kim, Kyung Mo; Caetano-Anollés, Gustavo; Nasir, Arshan

2017-01-01

Viruses can be classified into archaeoviruses, bacterioviruses, and eukaryoviruses according to the taxonomy of the infected host. The host-constrained perception of viruses implies preference of genetic exchange between viruses and cellular organisms of their host superkingdoms and viral origins from host cells either via escape or reduction. However, viruses frequently establish non-lytic interactions with organisms and endogenize into the genomes of bacterial endosymbionts that reside in eukaryotic cells. Such interactions create opportunities for genetic exchange between viruses and organisms of non-host superkingdoms. Here, we take an atypical approach to revisit virus-cell interactions by first identifying protein fold structures in the proteomes of archaeoviruses, bacterioviruses, and eukaryoviruses and second by tracing their spread in the proteomes of superkingdoms Archaea, Bacteria, and Eukarya. The exercise quantified protein structural homologies between viruses and organisms of their host and non-host superkingdoms and revealed likely candidates for virus-to-cell and cell-to-virus gene transfers. Unexpected lifestyle-driven genetic affiliations between bacterioviruses and Eukarya and eukaryoviruses and Bacteria were also predicted in addition to a large cohort of protein folds that were universally shared by viral and cellular proteomes and virus-specific protein folds not detected in cellular proteomes. These protein folds provide unique insights into viral origins and evolution that are generally difficult to recover with traditional sequence alignment-dependent evolutionary analyses owing to the fast mutation rates of viral gene sequences.

Quantitative proteomics and systems analysis of cultured H9C2 cardiomyoblasts during differentiation over time supports a 'function follows form' model of differentiation.

PubMed

Kankeu, Cynthia; Clarke, Kylie; Van Haver, Delphi; Gevaert, Kris; Impens, Francis; Dittrich, Anna; Roderick, H Llewelyn; Passante, Egle; Huber, Heinrich J

2018-05-17

The rat cardiomyoblast cell line H9C2 has emerged as a valuable tool for studying cardiac development, mechanisms of disease and toxicology. We present here a rigorous proteomic analysis that monitored the changes in protein expression during differentiation of H9C2 cells into cardiomyocyte-like cells over time. Quantitative mass spectrometry followed by gene ontology (GO) enrichment analysis revealed that early changes in H9C2 differentiation are related to protein pathways of cardiac muscle morphogenesis and sphingolipid synthesis. These changes in the proteome were followed later in the differentiation time-course by alterations in the expression of proteins involved in cation transport and beta-oxidation. Studying the temporal profile of the H9C2 proteome during differentiation in further detail revealed eight clusters of co-regulated proteins that can be associated with early, late, continuous and transient up- and downregulation. Subsequent reactome pathway analysis based on these eight clusters further corroborated and detailed the results of the GO analysis. Specifically, this analysis confirmed that proteins related to pathways in muscle contraction are upregulated early and transiently, and proteins relevant to extracellular matrix organization are downregulated early. In contrast, upregulation of proteins related to cardiac metabolism occurs at later time points. Finally, independent validation of the proteomics results by immunoblotting confirmed hereto unknown regulators of cardiac structure and ionic metabolism. Our results are consistent with a 'function follows form' model of differentiation, whereby early and transient alterations of structural proteins enable subsequent changes that are relevant to the characteristic physiology of cardiomyocytes.

Toxic effects of male Perna viridis gonad exposed to BaP, DDT and their mixture: A metabolomic and proteomic study of the underlying mechanism.

PubMed

Song, Qinqin; Zheng, Pengfei; Qiu, Liguo; Jiang, Xiu; Zhao, Hongwei; Zhou, Hailong; Han, Qian; Diao, Xiaoping

2016-01-05

Benzo(a)pyrene and dichlorodiphenyltrichloroethane are typical persistent organic pollutants, and also the widespread environmental estrogens with known toxicity towards green mussels Perna viridis. In this study, the toxicological effects of BaP and DDT and their mixture were assessed in green mussel gonads using proteomic and metabolomic approaches. Metabolomics by NMR spectroscopy revealed that BaP did not show obvious metabolite changes in the gonad of male green mussel. DDT mainly caused some disturbance of osmotic regulation and energy metabolism by changing BCAAs, alanine, threonine, arginine, etc., unknown metabolite (3.53 ppm), glycine, homarine and ATP at different levels. However, the mixture of BaP and DDT mainly caused some disturbance in osmotic regulation and energy metabolism by differentially altering branched chain amino acids, glutamate, alanine, arginine, unknown metabolite (3.53 ppm), glycine, 4-aminobutyrate, dimethylglycine, homarine and ATP. The results suggest that DDT alone may cause most of metabolites changes in the mixture exposed male mussel gonad, and the results also show that the male P. viridis gonad was more sensitive to DDT than BaP exposures. Proteomic study showed that BaP, DDT and their mixture may have different modes of action. Proteomic responses revealed that BaP induced signal transduction, oxidative stress, spermatogenesis, etc. in the male green mussel gonad; whereas DDT exposure altered proteins that were associated with signal transduction, oxidative stress, cytoskeleton and cell structure, cellular organization, energy metabolism, etc. However, the mixture of BaP and DDT affected proteins related to cytoskeleton and cell structure, oxidative stress, cellular organization, etc. This research demonstrated that metabolomic and proteomic approaches could better elucidate the underlying mechanism of environmental pollutants gonad toxicity. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

School and local authority characteristics associated with take-up of free school meals in Scottish secondary schools, 2014

PubMed Central

Chambers, Stephanie; Dundas, Ruth; Torsney, Ben

2016-01-01

School meals are an important state-delivered mechanism for improving children’s diets. Scottish local authorities have a statutory duty to provide free school meals (FSM) to families meeting means-testing criteria. Inevitably take-up of FSM does not reach 100%. Explanations put forward to explain this include social stigma, as well as a more general dissatisfaction amongst pupils about lack of modern facilities and meal quality, and a preference to eat where friends are eating. This study investigated characteristics associated with take-up across Scottish secondary schools in 2013–2014 using multilevel modelling techniques. Results suggest that stigma, food quality and the ability to eat with friends are associated with greater take-up. Levels of school modernisation appeared less important, as did differences between more urban or rural areas. Future studies should focus on additional school-level variables to identify characteristics associated with take-up, with the aim of reducing the number of registered pupils not taking-up FSM. PMID:28191363

Evidence for the Psychometric Validity, Internal Consistency and Measurement Invariance of Warwick Edinburgh Mental Well-being Scale Scores in Scottish and Irish Adolescents.

PubMed

McKay, Michael T; Andretta, James R

2017-09-01

Mental well-being is an important indicator of current, but also the future health of adolescents. The 14-item Warwick Edinburgh Mental Well-being Scale (WEMWBS) has been well validated in adults world-wide, but less work has been undertaken to examine the psychometric validity and internal consistency of WEMWBS scores in adolescents. In particular, little research has examined scores on the short 7-item version of the WEMWBS. The present study used two large samples of school children in Scotland and Northern Ireland and found that for both forms of the WEMWBS, scores were psychometrically valid, internally consistent, factor saturated, and measurement invariant by country. Using the WEMWBS full form, males reported significantly higher scores than females, and Northern Irish adolescents reported significantly higher scores than their Scottish counterparts. Last, the lowest overall levels of well-being were observed among Scottish females. Copyright © 2017. Published by Elsevier B.V.

Academic Self-Efficacy Partially Mediates the Relationship between Scottish Index of Multiple Deprivation and Composite Attainment Score.

PubMed

Perry, John L; Dempster, Martin; McKay, Michael T

2017-01-01

A developing literature continues to testify to the relationship between higher socio-economic status (SES) and better academic attainment. However, the literature is complex in terms of the variety of SES and attainment indicators used. Against the backdrop of a Scottish Government initiative to close the attainment gap between higher and lower SES children, the present study examined the relationship between individual-level Scottish Index of Multiple Deprivation (SIMD) and National Lower Tariff Score in school children in the West of Scotland. Results showed a practically significant relationship between SIMD and Tariff Score. This relationship was partially mediated by higher academic self-efficacy, so that higher belief in academic competency partially mediated the SIMD-Tariff Score relationship. Further, this partial mediation was robust to the influence of gender, sensation seeking, level of school attendance and past month frequency of Heavy Episodic Drinking. It is suggested that increasing attendance and perceived academic competence are viable ways (among others) of attempting to close the attainment gap.

[Claw size of Scottish Highland Cows after pasture and housing periods].

PubMed

Nuss, K; Kolp, E; Braun, U; Weidmann, E; Hässig, M

2014-09-01

The claws of pastured Scottish Highland Cattle are large and this may raise the question if regular claw trimming is necessary. Therefore, the claws of the right thoracic and pelvic limbs were measured in 22 Scottish Highland cows 4 times 8 weeks apart. The cows were kept on various alpine pastures before the first measurement, on a two-hectare low-land pasture before the second measurement, in a welfare-compliant straw-bedded free stall before the third measurement and on alpine pasture before the fourth measurement. Housing conditions significantly affected claw dimensions. The claws were composed of dry, hard horn during pasture periods, and had prominent weight-bearing hoof-wall borders and soles with a natural axial slope. Long dorsal walls and heels and a greater symmetry were common. Claw lesions were absent. In contrast, free-stall housing was associated with shorter toes and steeper toe angles, but white line deterioration, heel horn erosion, wearing of the axial slope and hoof wall edges were common.

Academic Self-Efficacy Partially Mediates the Relationship between Scottish Index of Multiple Deprivation and Composite Attainment Score

PubMed Central

Perry, John L.; Dempster, Martin; McKay, Michael T.

2017-01-01

A developing literature continues to testify to the relationship between higher socio-economic status (SES) and better academic attainment. However, the literature is complex in terms of the variety of SES and attainment indicators used. Against the backdrop of a Scottish Government initiative to close the attainment gap between higher and lower SES children, the present study examined the relationship between individual-level Scottish Index of Multiple Deprivation (SIMD) and National Lower Tariff Score in school children in the West of Scotland. Results showed a practically significant relationship between SIMD and Tariff Score. This relationship was partially mediated by higher academic self-efficacy, so that higher belief in academic competency partially mediated the SIMD-Tariff Score relationship. Further, this partial mediation was robust to the influence of gender, sensation seeking, level of school attendance and past month frequency of Heavy Episodic Drinking. It is suggested that increasing attendance and perceived academic competence are viable ways (among others) of attempting to close the attainment gap. PMID:29163281

School and local authority characteristics associated with take-up of free school meals in Scottish secondary schools, 2014.

PubMed

Chambers, Stephanie; Dundas, Ruth; Torsney, Ben

2016-01-02

School meals are an important state-delivered mechanism for improving children's diets. Scottish local authorities have a statutory duty to provide free school meals (FSM) to families meeting means-testing criteria. Inevitably take-up of FSM does not reach 100%. Explanations put forward to explain this include social stigma, as well as a more general dissatisfaction amongst pupils about lack of modern facilities and meal quality, and a preference to eat where friends are eating. This study investigated characteristics associated with take-up across Scottish secondary schools in 2013-2014 using multilevel modelling techniques. Results suggest that stigma, food quality and the ability to eat with friends are associated with greater take-up. Levels of school modernisation appeared less important, as did differences between more urban or rural areas. Future studies should focus on additional school-level variables to identify characteristics associated with take-up, with the aim of reducing the number of registered pupils not taking-up FSM.

Ladies from hell, Aberdeen free gardeners, and the Russian influenza: an anthropometric analysis of WWI-era Scottish soldiers and civilians.

PubMed

Riggs, Paul; Cuff, Timothy

2013-01-01

We analyze data on the height of Scottish men, both civilians and members of the military forces serving in World War I measured in the 1910s, in order to provide another window into the biological well-being of late nineteenth-century birth cohorts. The evidence indicates that rural residents still had a distinct height advantage over their urban counterparts and that military men displayed a slower growth profile than did civilians, but mean heights for the two groups of adults were similar. Mean stature for both groups is well above those found by Floud for British troops born in the 1880s and greater than that of Scottish convicts from the 1830s. Men who were in utero between 1889 and 1893 were slightly stunted, "marked for life" by an encounter with the Russian influenza which struck the region repeatedly. Copyright © 2012 Elsevier B.V. All rights reserved.

A new version of the HBSC Family Affluence Scale - FAS III: Scottish Qualitative Findings from the International FAS Development Study.

PubMed

Hartley, Jane E K; Levin, Kate; Currie, Candace

A critical review of the Family Affluence Scale (FAS) concluded that FAS II was no longer discriminatory within very rich or very poor countries, where a very high or a very low proportion of children were categorised as high FAS or low FAS respectively (Currie et al. 2008). The review concluded that a new version of FAS - FAS III - should be developed to take into account current trends in family consumption patterns across the European region, the US and Canada. In 2012, the FAS Development and Validation Study was conducted in eight countries - Denmark, Greenland, Italy, Norway, Poland, Romania, Slovakia and Scotland. This paper describes the Scottish qualitative findings from this study. The Scottish qualitative fieldwork comprising cognitive interviews and focus groups sampled from 11, 13 and 15 year-old participants from 18 of the most- and least- economically deprived schools. These qualitative results were used to inform the final FAS III recommendations.

Proteoglycomics: Recent Progress and Future Challenges

PubMed Central

Ly, Mellisa; Laremore, Tatiana N.

2010-01-01

Abstract Proteoglycomics is a systematic study of structure, expression, and function of proteoglycans, a posttranslationally modified subset of a proteome. Although relying on the established technologies of proteomics and glycomics, proteoglycomics research requires unique approaches for elucidating structure–function relationships of both proteoglycan components, glycosaminoglycan chain, and core protein. This review discusses our current understanding of structure and function of proteoglycans, major players in the development, normal physiology, and disease. A brief outline of the proteoglycomic sample preparation and analysis is provided along with examples of several recent proteoglycomic studies. Unique challenges in the characterization of glycosaminoglycan component of proteoglycans are discussed, with emphasis on the many analytical tools used and the types of information they provide. PMID:20450439

In-depth proteomic analysis of Varroa destructor: Detection of DWV-complex, ABPV, VdMLV and honeybee proteins in the mite.

PubMed

Erban, Tomas; Harant, Karel; Hubalek, Martin; Vitamvas, Pavel; Kamler, Martin; Poltronieri, Palmiro; Tyl, Jan; Markovic, Martin; Titera, Dalibor

2015-09-11

We investigated pathogens in the parasitic honeybee mite Varroa destructor using nanoLC-MS/MS (TripleTOF) and 2D-E-MS/MS proteomics approaches supplemented with affinity-chromatography to concentrate trace target proteins. Peptides were detected from the currently uncharacterized Varroa destructor Macula-like virus (VdMLV), the deformed wing virus (DWV)-complex and the acute bee paralysis virus (ABPV). Peptide alignments revealed detection of complete structural DWV-complex block VP2-VP1-VP3, VDV-1 helicase and single-amino-acid substitution A/K/Q in VP1, the ABPV structural block VP1-VP4-VP2-VP3 including uncleaved VP4/VP2, and VdMLV coat protein. Isoforms of viral structural proteins of highest abundance were localized via 2D-E. The presence of all types of capsid/coat proteins of a particular virus suggested the presence of virions in Varroa. Also, matches between the MWs of viral structural proteins on 2D-E and their theoretical MWs indicated that viruses were not digested. The absence/scarce detection of non-structural proteins compared with high-abundance structural proteins suggest that the viruses did not replicate in the mite; hence, virions accumulate in the Varroa gut via hemolymph feeding. Hemolymph feeding also resulted in the detection of a variety of honeybee proteins. The advantages of MS-based proteomics for pathogen detection, false-positive pathogen detection, virus replication, posttranslational modifications, and the presence of honeybee proteins in Varroa are discussed.

In-depth proteomic analysis of Varroa destructor: Detection of DWV-complex, ABPV, VdMLV and honeybee proteins in the mite

PubMed Central

Erban, Tomas; Harant, Karel; Hubalek, Martin; Vitamvas, Pavel; Kamler, Martin; Poltronieri, Palmiro; Tyl, Jan; Markovic, Martin; Titera, Dalibor

2015-01-01

We investigated pathogens in the parasitic honeybee mite Varroa destructor using nanoLC-MS/MS (TripleTOF) and 2D-E-MS/MS proteomics approaches supplemented with affinity-chromatography to concentrate trace target proteins. Peptides were detected from the currently uncharacterized Varroa destructor Macula-like virus (VdMLV), the deformed wing virus (DWV)-complex and the acute bee paralysis virus (ABPV). Peptide alignments revealed detection of complete structural DWV-complex block VP2-VP1-VP3, VDV-1 helicase and single-amino-acid substitution A/K/Q in VP1, the ABPV structural block VP1-VP4-VP2-VP3 including uncleaved VP4/VP2, and VdMLV coat protein. Isoforms of viral structural proteins of highest abundance were localized via 2D-E. The presence of all types of capsid/coat proteins of a particular virus suggested the presence of virions in Varroa. Also, matches between the MWs of viral structural proteins on 2D-E and their theoretical MWs indicated that viruses were not digested. The absence/scarce detection of non-structural proteins compared with high-abundance structural proteins suggest that the viruses did not replicate in the mite; hence, virions accumulate in the Varroa gut via hemolymph feeding. Hemolymph feeding also resulted in the detection of a variety of honeybee proteins. The advantages of MS-based proteomics for pathogen detection, false-positive pathogen detection, virus replication, posttranslational modifications, and the presence of honeybee proteins in Varroa are discussed. PMID:26358842

Two tales of cardiovascular risks—middle-aged women living in Sweden and Scotland: a cross-sectional comparative study

PubMed Central

Wennerholm, Carina; Bromley, Catherine; Johansson, AnnaKarin; Nilsson, Staffan; Frank, John; Faresjö, Tomas

2017-01-01

Objectives To compare cardiovascular risk factors as well as rates of cardiovascular diseases in middle-aged women from urban areas in Scotland and Sweden. Design Comparative cross-sectional study. Setting Data from the general population in urban areas of Scotland and the general population in two major Swedish cities in southeast Sweden, south of Stockholm. Participants Comparable data of middle-aged women (40–65 years) from the Scottish Health Survey (n=6250) and the Swedish QWIN study (n=741) were merged together into a new dataset (n=6991 participants). Main outcome measure We compared middle-aged women in urban areas in Sweden and Scotland regarding risk factors for cardiovascular disease (CVD), CVD diagnosis, anthropometrics, psychological distress and lifestyle. Results In almost all measurements, there were significant differences between the countries, favouring the Swedish women. Scottish women demonstrated a higher frequency of alcohol consumption, smoking, obesity, low vegetable consumption, a sedentary lifestyle and also more psychological distress. For doctor-diagnosed coronary heart disease, there were also significant differences, with a higher prevalence among the Scottish women. Conclusions This is one of the first studies that clearly shows that Scottish middle-aged women are particularly affected by a worse profile of CVD risks. The profound differences in CVD risk and outcome frequency in the two populations are likely to have arisen from differences in the two groups of women's social, cultural, political and economic environments. PMID:28790040

Public Health and Unconventional Oil and Gas Extraction Including Fracking: Global Lessons from a Scottish Government Review

PubMed Central

Watterson, Andrew

2018-01-01

Unconventional oil and gas extraction (UOGE) including fracking for shale gas is underway in North America on a large scale, and in Australia and some other countries. It is viewed as a major source of global energy needs by proponents. Critics consider fracking and UOGE an immediate and long-term threat to global, national, and regional public health and climate. Rarely have governments brought together relatively detailed assessments of direct and indirect public health risks associated with fracking and weighed these against potential benefits to inform a national debate on whether to pursue this energy route. The Scottish government has now done so in a wide-ranging consultation underpinned by a variety of reports on unconventional gas extraction including fracking. This paper analyses the Scottish government approach from inception to conclusion, and from procedures to outcomes. The reports commissioned by the Scottish government include a comprehensive review dedicated specifically to public health as well as reports on climate change, economic impacts, transport, geology, and decommissioning. All these reports are relevant to public health, and taken together offer a comprehensive review of existing evidence. The approach is unique globally when compared with UOGE assessments conducted in the USA, Australia, Canada, and England. The review process builds a useful evidence base although it is not without flaws. The process approach, if not the content, offers a framework that may have merits globally. PMID:29617318

Constructing Proteome Reference Map of the Porcine Jejunal Cell Line (IPEC-J2) by Label-Free Mass Spectrometry.

PubMed

Kim, Sang Hoon; Pajarillo, Edward Alain B; Balolong, Marilen P; Lee, Ji Yoon; Kang, Dae-Kyung

2016-06-28

In this study, the global proteome of the IPEC-J2 cell line was evaluated using ultra-high performance liquid chromatography coupled to a quadrupole Q Exactive™ Orbitrap mass spectrometer. Proteins were isolated from highly confluent IPEC-J2 cells in biological replicates and analyzed by label-free mass spectrometry prior to matching against a porcine genomic dataset. The results identified 1,517 proteins, accounting for 7.35% of all genes in the porcine genome. The highly abundant proteins detected, such as actin, annexin A2, and AHNAK nucleoprotein, are involved in structural integrity, signaling mechanisms, and cellular homeostasis. The high abundance of heat shock proteins indicated their significance in cellular defenses, barrier function, and gut homeostasis. Pathway analysis and annotation using the Kyoto Encyclopedia of Genes and Genomes database resulted in a putative protein network map of the regulation of immunological responses and structural integrity in the cell line. The comprehensive proteome analysis of IPEC-J2 cells provides fundamental insights into overall protein expression and pathway dynamics that might be useful in cell adhesion studies and immunological applications.

Proteomic analysis of skeletal organic matrix from the stony coral Stylophora pistillata

PubMed Central

Drake, Jeana L.; Mass, Tali; Haramaty, Liti; Zelzion, Ehud; Bhattacharya, Debashish; Falkowski, Paul G.

2013-01-01

It has long been recognized that a suite of proteins exists in coral skeletons that is critical for the oriented precipitation of calcium carbonate crystals, yet these proteins remain poorly characterized. Using liquid chromatography-tandem mass spectrometry analysis of proteins extracted from the cell-free skeleton of the hermatypic coral, Stylophora pistillata, combined with a draft genome assembly from the cnidarian host cells of the same species, we identified 36 coral skeletal organic matrix proteins. The proteome of the coral skeleton contains an assemblage of adhesion and structural proteins as well as two highly acidic proteins that may constitute a unique coral skeletal organic matrix protein subfamily. We compared the 36 skeletal organic matrix protein sequences to genome and transcriptome data from three other corals, three additional invertebrates, one vertebrate, and three single-celled organisms. This work represents a unique extensive proteomic analysis of biomineralization-related proteins in corals from which we identify a biomineralization “toolkit,” an organic scaffold upon which aragonite crystals can be deposited in specific orientations to form a phenotypically identifiable structure. PMID:23431140

Exploring the Spatial and Temporal Organization of a Cell’s Proteome

PubMed Central

Beck, Martin; Topf, Maya; Frazier, Zachary; Tjong, Harianto; Xu, Min; Zhang, Shihua; Alber, Frank

2013-01-01

To increase our current understanding of cellular processes, such as cell signaling and division, knowledge is needed about the spatial and temporal organization of the proteome at different organizational levels. These levels cover a wide range of length and time scales: from the atomic structures of macromolecules for inferring their molecular function, to the quantitative description of their abundance, and distribution in the cell. Emerging new experimental technologies are greatly increasing the availability of such spatial information on the molecular organization in living cells. This review addresses three fields that have significantly contributed to our understanding of the proteome’s spatial and temporal organization: first, methods for the structure determination of individual macromolecular assemblies, specifically the fitting of atomic structures into density maps generated from electron microscopy techniques; second, research that visualizes the spatial distributions of these complexes within the cellular context using cryo electron tomography techniques combined with computational image processing; and third, methods for the spatial modeling of the dynamic organization of the proteome, specifically those methods for simulating reaction and diffusion of proteins and complexes in crowded intracellular fluids. The long-term goal is to integrate the varied data about a proteome’s organization into a spatially explicit, predictive model of cellular processes. PMID:21094684

ABCD2 identifies a subclass of peroxisomes in mouse adipose tissue

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Xiaoxi, E-mail: xiaoxi.liu@uky.edu; Liu, Jingjing, E-mail: jingjing.liu0@gmail.com; Lester, Joshua D., E-mail: joshua.lester@uky.edu

2015-01-02

Highlights: • We examined the D2 localization and the proteome of D2-containing compartment in mouse adipose tissue. • We confirmed the presence of D2 on a subcellular compartment that has typical structure as a microperoxisome. • We demonstrated the scarcity of peroxisome markers on D2-containing compartment. • The D2-containing compartment may be a subpopulation of peroxisome in mouse adipose tissue. • Proteomic data suggests potential association between D2-containing compartment and mitochondria and ER. - Abstract: ATP-binding cassette transporter D2 (D2) is an ABC half transporter that is thought to promote the transport of very long-chain fatty acyl-CoAs into peroxisomes. Bothmore » D2 and peroxisomes increase during adipogenesis. Although peroxisomes are essential to both catabolic and anabolic lipid metabolism, their function, and that of D2, in adipose tissues remain largely unknown. Here, we investigated the D2 localization and the proteome of D2-containing organelles, in adipose tissue. Centrifugation of mouse adipose homogenates generated a fraction enriched with D2, but deficient in peroxisome markers including catalase, PEX19, and ABCD3 (D3). Electron microscopic imaging of this fraction confirmed the presence of D2 protein on an organelle with a dense matrix and a diameter of ∼200 nm, the typical structure and size of a microperoxisome. D2 and PEX19 antibodies recognized distinct structures in mouse adipose. Immunoisolation of the D2-containing compartment confirmed the scarcity of PEX19 and proteomic profiling revealed the presence of proteins associated with peroxisome, endoplasmic reticulum (ER), and mitochondria. D2 is localized to a distinct class of peroxisomes that lack many peroxisome proteins, and may associate physically with mitochondria and the ER.« less

Structural brain MRI trait polygenic score prediction of cognitive abilities

PubMed Central

Luciano, Michelle; Marioni, Riccardo E; Hernández, Maria Valdés; Maniega, Susana Munoz; Hamilton, Iona F; Royle, Natalie A.; Scotland, Generation; Chauhan, Ganesh; Bis, Joshua C.; Debette, Stephanie; DeCarli, Charles; Fornage, Myriam; Schmidt, Reinhold; Ikram, M. Arfan; Launer, Lenore J.; Seshadri, Sudha; Bastin, Mark E.; Porteous, David J.; Wardlaw, Joanna; Deary, Ian J

2016-01-01

Structural brain magnetic resonance imaging (MRI) traits share part of their genetic variance with cognitive traits. Here, we use genetic association results from large meta-analytic studies of genome-wide association for brain infarcts, white matter hyperintensities, intracranial, hippocampal and total brain volumes to estimate polygenic scores for these traits in three Scottish samples: Generation Scotland: Scottish Family Health Study (GS:SFHS), and the Lothian Birth Cohorts of 1936 (LBC1936) and 1921 (LBC1921). These five brain MRI trait polygenic scores were then used to 1) predict corresponding MRI traits in the LBC1936 (numbers ranged 573 to 630 across traits) and 2) predict cognitive traits in all three cohorts (in 8,115 to 8,250 persons). In the LBC1936, all MRI phenotypic traits were correlated with at least one cognitive measure; and polygenic prediction of MRI traits was observed for intracranial volume. Meta-analysis of the correlations between MRI polygenic scores and cognitive traits revealed a significant negative correlation (maximal r=0.08) between the hippocampal volume polygenic score and measures of global cognitive ability collected in childhood and in old age in the Lothian Birth Cohorts. The lack of association to a related general cognitive measure when including the GS:SFHS points to either type 1 error or the importance of using prediction samples that closely match the demographics of the genome-wide association samples from which prediction is based. Ideally, these analyses should be repeated in larger samples with data on both MRI and cognition, and using MRI GWA results from even larger meta-analysis studies. PMID:26427786

Income-related inequity in the use of GP services by children: a comparison of Ireland and Scotland.

PubMed

Layte, Richard; Nolan, Anne

2015-06-01

Equity of access to health care is a key component of national and international health policy, with most countries subscribing to the principle that health care should be allocated on the basis of need, rather than ability to pay or other criteria. The issue of health care entitlements for children is particularly pertinent given the strong causal links that have been demonstrated between eligibility for free care, utilisation and health outcomes. The Irish health care system is unusual in requiring the majority of the population to pay the full out-of-pocket cost of GP care. In contrast, all Scottish residents are entitled to free GP care at the point of use. This difference in public health care entitlements between Ireland and Scotland allows us to examine the impact of differences in financing structures on equity in GP care. In this paper, we use data from two nationally representative surveys of children in Ireland and Scotland to examine the degree of income-related inequity in the utilisation of GP services in both countries. We find that while the distribution of GP care is significantly pro-poor in Ireland, even after adjustment for health need, there is little or no significant inequity in GP utilisation among Scottish children. However, focusing just on children who pay the full price of GP care in Ireland, we find some evidence for a significant pro-rich distribution of GP visits. These results reflect the particular structure of health care entitlements that exist in two systems.

Novel microclimate monitoring and microbial colonisation in sandstones of historic buildings, Glasgow, Scotland

NASA Astrophysics Data System (ADS)

Duthie, L.; Hyslop, E.; Lee, M.; Phoenix, V.; Kennedy, C.

2009-04-01

The impact of our changing climate on the historic built environment of Scotland has received surprisingly little attention. Current projections indicate that Scotland will become notably wetter and warmer over the coming decades. Winter temperatures are predicted to increase by 30C with 15% more precipitation, one result should be more aggressive microbial weathering of the sandstone buildings. In order to understand better and to quantify the damage potentially caused, it is necessary to analyse existing microbial populations but also to characterize conditions within building stones, how they change over diurnal and seasonal cycles, and how they differ from external conditions. In this study, temperature, humidity and moisture sensors were inserted at different depths into representative Scottish sandstones to record parameters key to microbial colonisation and organic weathering. Penetration of photosynthetically active radiation has also been measured. The within-stone data were compared to meteorological conditions recorded by an adjacent weather station. These data have then been compared with analysis of the microbial populations at different depths within the stone, using osmium stained polished blocks. Notably, microbes occur up to 7 mm beneath the outer sandstone surface, with community structure differing with depth. Clearly, different communities experience very different conditions within the stone, reflecting trophic structure, light penetration and microclimate. The sensor data confirm that temperature and water availability all vary within the stone and differ considerably with the external environment. We conclude that the warm and humid microclimate within Scottish building stones promotes microbial colonisation and stone decay and both will increase significantly with the changing climate of Scotland and north-west Europe.

Representations of minimum unit pricing for alcohol in UK newspapers: a case study of a public health policy debate.

PubMed

Patterson, Chris; Katikireddi, Srinivasa Vittal; Wood, Karen; Hilton, Shona

2015-03-01

Mass media influence public acceptability, and hence feasibility, of public health interventions. This study investigates newsprint constructions of the alcohol problem and minimum unit pricing (MUP). Quantitative content analysis of 901 articles about MUP published in 10 UK and Scottish newspapers between 2005 and 2012. MUP was a high-profile issue, particularly in Scottish publications. Reporting increased steadily between 2008 and 2012, matching the growing status of the debate. The alcohol problem was widely acknowledged, often associated with youths, and portrayed as driven by cheap alcohol, supermarkets and drinking culture. Over-consumption was presented as a threat to health and social order. Appraisals of MUP were neutral, with supportiveness increasing slightly over time. Arguments focused on health impacts more frequently than more emotive perspectives or business interests. Health charities and the NHS were cited slightly more frequently than alcohol industry representatives. Emphases on efficacy, evidence and experts are positive signs for evidence-based policymaking. The high profile of MUP, along with growing support within articles, could reflect growing appetite for action on the alcohol problem. Representations of the problem as structurally driven might engender support for legislative solutions, although cultural explanations remain common. © The Author 2014. Published by Oxford University Press on behalf of Faculty of Public Health.

Representations of minimum unit pricing for alcohol in UK newspapers: a case study of a public health policy debate

PubMed Central

Patterson, Chris; Katikireddi, Srinivasa Vittal; Wood, Karen; Hilton, Shona

2015-01-01

Background Mass media influence public acceptability, and hence feasibility, of public health interventions. This study investigates newsprint constructions of the alcohol problem and minimum unit pricing (MUP). Methods Quantitative content analysis of 901 articles about MUP published in 10 UK and Scottish newspapers between 2005 and 2012. Results MUP was a high-profile issue, particularly in Scottish publications. Reporting increased steadily between 2008 and 2012, matching the growing status of the debate. The alcohol problem was widely acknowledged, often associated with youths, and portrayed as driven by cheap alcohol, supermarkets and drinking culture. Over-consumption was presented as a threat to health and social order. Appraisals of MUP were neutral, with supportiveness increasing slightly over time. Arguments focused on health impacts more frequently than more emotive perspectives or business interests. Health charities and the NHS were cited slightly more frequently than alcohol industry representatives. Conclusion Emphases on efficacy, evidence and experts are positive signs for evidence-based policymaking. The high profile of MUP, along with growing support within articles, could reflect growing appetite for action on the alcohol problem. Representations of the problem as structurally driven might engender support for legislative solutions, although cultural explanations remain common. PMID:25312002

Paediatric burns in LMICs: An evaluation of the barriers and facilitators faced by staff involved in burns education training programmes in Blantyre, Malawi.

PubMed

Harris, Lyndsey; Fioratou, Evridiki; Broadis, Emily

2016-08-01

A burn prevention and education programme - the Reduction of Burn and Scald Mortality and Morbidity in Children in Malawi project - was implemented from January 2010-2013 in Queen Elizabeth Central Hospital, Malawi. This study aimed to investigate the barriers and facilitators of implementing education-training programmes. Semi-structured interviews with 14 Scottish and Malawian staff delivering and receiving teaching at training education programmes were conducted. All interviews were recorded, transcribed and analysed using thematic analysis. Overarching barriers and facilitators were similar for both sets of staff. Scottish participants recognised that limited experience working in LMICs narrowed the challenges they anticipated. Time was a significant barrier to implementation of training courses for both sets of participants. Lack of hands on practical experience was the greatest barrier to implementing the skills learnt for Malawian staff. Sustainability was a significant facilitator to successful implementation of training programmes. Encouraging involvement of Malawian staff in the co-ordination and delivery of teaching enabled those who attend courses to teach others. A recognition of and response to the barriers and facilitators associated with introducing paediatric burn education training programmes can contribute to the development of sustainable programme implementation in Malawi and other LMICs. Copyright © 2015 Elsevier Ltd and ISBI. All rights reserved.

Low-Impact Exploration for Gold in the Scottish Caledonides.

NASA Astrophysics Data System (ADS)

Rice, Samuel; Cuthbert, Simon; Hursthouse, Andrew; Broetto, Gabriele

2017-04-01

The Caledonian orogenic belt of the northern British Isles hosts some significant gold deposits. However, gold mineralization in the region is underexplored. Some of the most prospective areas identified by rich alluvial gold anomalies are environmentally and culturally sensitive. Traditional mineral exploration methods can have a range of negative environmental, social and economic impacts. The regional tourism economy is dependent on outdoor activities, landscape quality, wildlife and industrial heritage and has the potential to be disrupted by mineral resource developments. Low-cost, low-impact exploration strategies are therefore, key to sustainably developing the mineral resource potential. Research currently in progress in part of the Scottish Caledonides aims to develop protocols for more sustainable exploration. We are using a range of geoscience techniques to characterize the mineral system, improve exploration targeting and reduce negative impacts. To do this we targeted an area with a large preexisting dataset (e.g. stream sediment geochemistry, geomorphology, structural geology, petrology, geophysics, mine data) that can be synthesized and analyzed in a GIS. Part of the work aims to develop and test a model for gold dispersion in the surface environment that accounts for climatic and anthropogenic influences in order to locate bedrock sources. This multidisciplinary approach aims to reduce the target areas for subsequent exploration activities such as soil sampling, excavation and drilling.

Locals, incomers and intra-national migration: place-identities and a Scottish island.

PubMed

McKinlay, Andy; McVittie, Chris

2007-03-01

In a trans-national context, immigrants are often described as essentially different from existing residents. However these descriptions of group differences are occasioned constructions of immigrants, and talk about nations provides frameworks of history and space within which immigration is understood. Claimed group differences and the proposed commonality of nation together present a challenging context for immigrants to negotiate identities and to gain acceptance. Drawing on the concept of place-identity, we examined here whether similar issues arise in intra-national migration to a remote Scottish island. We conducted semi-structured interviews with individuals who had lived on the island for periods ranging from 14 months to 20 years. The interviewees described island residents as comprising different groups, in terms such as residence, motivation, place of birth, and connections to other locations. The interviewees negotiated place-identities that compared favourably with others with more transitory connections but unfavourably with residents of longer-standing. Findings show that spatial connections can be used to account for varying degrees of social status in such locations. But some issues relevant to trans-national immigration still arise in intra-national migration, even in the absence of racial, ethnic, religious, or language differences. In short, 'incomers' cannot readily do 'being local'.

The proteomic complexity and rise of the primordial ancestor of diversified life

PubMed Central

2011-01-01

Background The last universal common ancestor represents the primordial cellular organism from which diversified life was derived. This urancestor accumulated genetic information before the rise of organismal lineages and is considered to be either a simple 'progenote' organism with a rudimentary translational apparatus or a more complex 'cenancestor' with almost all essential biological processes. Recent comparative genomic studies support the latter model and propose that the urancestor was similar to modern organisms in terms of gene content. However, most of these studies were based on molecular sequences, which are fast evolving and of limited value for deep evolutionary explorations. Results Here we engage in a phylogenomic study of protein domain structure in the proteomes of 420 free-living fully sequenced organisms. Domains were defined at the highly conserved fold superfamily (FSF) level of structural classification and an iterative phylogenomic approach was used to reconstruct max_set and min_set FSF repertoires as upper and lower bounds of the urancestral proteome. While the functional make up of the urancestral sets was complex, they represent only 5-11% of the 1,420 FSFs of extant proteomes and their make up and reuse was at least 5 and 3 times smaller than proteomes of free-living organisms, repectively. Trees of proteomes reconstructed directly from FSFs or from molecular functions, which included the max_set and min_set as articial taxa, showed that urancestors were always placed at their base and rooted the tree of life in Archaea. Finally, a molecular clock of FSFs suggests the min_set reflects urancestral genetic make up more reliably and confirms diversified life emerged about 2.9 billion years ago during the start of planet oxygenation. Conclusions The minimum urancestral FSF set reveals the urancestor had advanced metabolic capabilities, was especially rich in nucleotide metabolism enzymes, had pathways for the biosynthesis of membrane sn1,2 glycerol ester and ether lipids, and had crucial elements of translation, including a primordial ribosome with protein synthesis capabilities. It lacked however fundamental functions, including transcription, processes for extracellular communication, and enzymes for deoxyribonucleotide synthesis. Proteomic history reveals the urancestor is closer to a simple progenote organism but harbors a rather complex set of modern molecular functions. PMID:21612591

Identification of new intrinsic proteins in Arabidopsis plasma membrane proteome.

PubMed

Marmagne, Anne; Rouet, Marie-Aude; Ferro, Myriam; Rolland, Norbert; Alcon, Carine; Joyard, Jacques; Garin, Jérome; Barbier-Brygoo, Hélène; Ephritikhine, Geneviève

2004-07-01

Identification and characterization of anion channel genes in plants represent a goal for a better understanding of their central role in cell signaling, osmoregulation, nutrition, and metabolism. Though channel activities have been well characterized in plasma membrane by electrophysiology, the corresponding molecular entities are little documented. Indeed, the hydrophobic protein equipment of plant plasma membrane still remains largely unknown, though several proteomic approaches have been reported. To identify new putative transport systems, we developed a new proteomic strategy based on mass spectrometry analyses of a plasma membrane fraction enriched in hydrophobic proteins. We produced from Arabidopsis cell suspensions a highly purified plasma membrane fraction and characterized it in detail by immunological and enzymatic tests. Using complementary methods for the extraction of hydrophobic proteins and mass spectrometry analyses on mono-dimensional gels, about 100 proteins have been identified, 95% of which had never been found in previous proteomic studies. The inventory of the plasma membrane proteome generated by this approach contains numerous plasma membrane integral proteins, one-third displaying at least four transmembrane segments. The plasma membrane localization was confirmed for several proteins, therefore validating such proteomic strategy. An in silico analysis shows a correlation between the putative functions of the identified proteins and the expected roles for plasma membrane in transport, signaling, cellular traffic, and metabolism. This analysis also reveals 10 proteins that display structural properties compatible with transport functions and will constitute interesting targets for further functional studies.

Single-molecule protein sequencing through fingerprinting: computational assessment

NASA Astrophysics Data System (ADS)

Yao, Yao; Docter, Margreet; van Ginkel, Jetty; de Ridder, Dick; Joo, Chirlmin

2015-10-01

Proteins are vital in all biological systems as they constitute the main structural and functional components of cells. Recent advances in mass spectrometry have brought the promise of complete proteomics by helping draft the human proteome. Yet, this commonly used protein sequencing technique has fundamental limitations in sensitivity. Here we propose a method for single-molecule (SM) protein sequencing. A major challenge lies in the fact that proteins are composed of 20 different amino acids, which demands 20 molecular reporters. We computationally demonstrate that it suffices to measure only two types of amino acids to identify proteins and suggest an experimental scheme using SM fluorescence. When achieved, this highly sensitive approach will result in a paradigm shift in proteomics, with major impact in the biological and medical sciences.

Identification of Missing Proteins Defined by Chromosome-Centric Proteome Project in the Cytoplasmic Detergent-Insoluble Proteins.

PubMed

Chen, Yang; Li, Yaxing; Zhong, Jiayong; Zhang, Jing; Chen, Zhipeng; Yang, Lijuan; Cao, Xin; He, Qing-Yu; Zhang, Gong; Wang, Tong

2015-09-04

Finding protein evidence (PE) for protein coding genes is a primary task of the Phase I Chromosome-Centric Human Proteome Project (C-HPP). Currently, there are 2948 PE level 2-4 coding genes per neXtProt, which are deemed missing proteins in the human proteome. As most samples prepared and analyzed in the C-HPP framework were focusing on detergent soluble proteins, we posit that as a natural composition the cytoplasmic detergent-insoluble proteins (DIPs) represent a source of finding missing proteins. We optimized a workflow and separated cytoplasmic DIPs from three human lung and three human hepatoma cell lines via differential speed centrifugation. We verified that the detergent-soluble proteins (DSPs) could be sufficiently depleted and the cytoplasmic DIP isolation was partially reproducible with Spearman r > 0.70 according to two independent SILAC MS experiments. Through label-free MS, we identified 4524 and 4156 DIPs from lung and liver cells, respectively. Among them, a total of 23 missing proteins (22 PE2 and 1 PE4) were identified by MS, and 18 of them had translation evidence; in addition, six PE5 proteins were identified by MS, three with translation evidence. We showed that cytoplasmic DIPs were not an enrichment of transmembrane proteins and were chromosome-, cell type-, and tissue-specific. Furthermore, we demonstrated that DIPs were distinct from DSPs in terms of structural and physical-chemical features. In conclusion, we have found 23 missing proteins and 6 PE5 proteins from the cytoplasmic insoluble proteome that is biologically and physical-chemically different from the soluble proteome, suggesting that cytoplasmic DIPs carry comprehensive and valuable information for finding PE of missing proteins. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD001694.

Caenorhabditis elegans chemical biology: lessons from small molecules

USDA-ARS?s Scientific Manuscript database

How can we complement Caenorhabditis elegans genomics and proteomics with a comprehensive structural and functional annotation of its metabolome? Several lines of evidence indicate that small molecules of largely undetermined structure play important roles in C. elegans biology, including key pathw...

Golgi Enrichment and Proteomic Analysis of Developing Pinus radiata Xylem by Free-Flow Electrophoresis

PubMed Central

Macdonald, Lucy J.; Adams, Paul D.; Petzold, Christopher J.; Strabala, Timothy J.; Wagner, Armin; Heazlewood, Joshua L.

2013-01-01

Our understanding of the contribution of Golgi proteins to cell wall and wood formation in any woody plant species is limited. Currently, little Golgi proteomics data exists for wood-forming tissues. In this study, we attempted to address this issue by generating and analyzing Golgi-enriched membrane preparations from developing xylem of compression wood from the conifer Pinus radiata. Developing xylem samples from 3-year-old pine trees were harvested for this purpose at a time of active growth and subjected to a combination of density centrifugation followed by free flow electrophoresis, a surface charge separation technique used in the enrichment of Golgi membranes. This combination of techniques was successful in achieving an approximately 200-fold increase in the activity of the Golgi marker galactan synthase and represents a significant improvement for proteomic analyses of the Golgi from conifers. A total of thirty known Golgi proteins were identified by mass spectrometry including glycosyltransferases from gene families involved in glucomannan and glucuronoxylan biosynthesis. The free flow electrophoresis fractions of enriched Golgi were highly abundant in structural proteins (actin and tubulin) indicating a role for the cytoskeleton during compression wood formation. The mass spectrometry proteomics data associated with this study have been deposited to the ProteomeXchange with identifier PXD000557. PMID:24416096

The Urine Proteome as a Biomarker of Radiation Injury: Submitted to Proteomics- Clinical Applications Special Issue: "Renal and Urinary Proteomics (Thongboonkerd)"

PubMed

Sharma, Mukut; Halligan, Brian D; Wakim, Bassam T; Savin, Virginia J; Cohen, Eric P; Moulder, John E

2008-06-18

Terrorist attacks or nuclear accidents could expose large numbers of people to ionizing radiation, and early biomarkers of radiation injury would be critical for triage, treatment and follow-up of such individuals. However, no such biomarkers have yet been proven to exist. We tested the potential of high throughput proteomics to identify protein biomarkers of radiation injury after total body X-ray irradiation in a rat model. Subtle functional changes in the kidney are suggested by an increased glomerular permeability for macromolecules measured within 24 hours after TBI. Ultrastructural changes in glomerular podocytes include partial loss of the interdigitating organization of foot processes. Analysis of urine by LC-MS/MS and 2D-GE showed significant changes in the urine proteome within 24 hours after TBI. Tissue kallikrein 1-related peptidase, cysteine proteinase inhibitor cystatin C and oxidized histidine were found to be increased while a number of proteinase inhibitors including kallikrein-binding protein and albumin were found to be decreased post-irradiation. Thus, TBI causes immediately detectable changes in renal structure and function and in the urinary protein profile. This suggests that both systemic and renal changes are induced by radiation and it may be possible to identify a set of biomarkers unique to radiation injury.

Proteomics of Dense Core Secretory Vesicles Reveal Distinct Protein Categories for Secretion of Neuroeffectors for Cell-Cell Communication

PubMed Central

Wegrzyn, Jill L.; Bark, Steven J.; Funkelstein, Lydiane; Mosier, Charles; Yap, Angel; Kazemi-Esfarjani, Parasa; La Spada, Albert; Sigurdson, Christina; O’Connor, Daniel T.; Hook, Vivian

2010-01-01

Regulated secretion of neurotransmitters and neurohumoural factors from dense core secretory vesicles provides essential neuroeffectors for cell-cell communication in the nervous and endocrine systems. This study provides comprehensive proteomic characterization of the categories of proteins in chromaffin dense core secretory vesicles that participate in cell-cell communication from the adrenal medulla. Proteomic studies were conducted by nano-HPLC Chip MS/MS tandem mass spectrometry. Results demonstrate that these secretory vesicles contain proteins of distinct functional categories consisting of neuropeptides and neurohumoural factors, protease systems, neurotransmitter enzymes and transporters, receptors, enzymes for biochemical processes, reduction/oxidation regulation, ATPases, protein folding, lipid biochemistry, signal transduction, exocytosis, calcium regulation, as well as structural and cell adhesion proteins. The secretory vesicle proteomic data identified 371 distinct proteins in the soluble fraction and 384 distinct membrane proteins, for a total of 686 distinct secretory vesicle proteins. Notably, these proteomic analyses illustrate the presence of several neurological disease-related proteins in these secretory vesicles, including huntingtin interacting protein, cystatin C, ataxin 7, and prion protein. Overall, these findings demonstrate that multiple protein categories participate in dense core secretory vesicles for production, storage, and secretion of bioactive neuroeffectors for cell-cell communication in health and disease. PMID:20695487

Progressive muscle proteome changes in a clinically relevant pig model of Duchenne muscular dystrophy.

PubMed

Fröhlich, Thomas; Kemter, Elisabeth; Flenkenthaler, Florian; Klymiuk, Nikolai; Otte, Kathrin A; Blutke, Andreas; Krause, Sabine; Walter, Maggie C; Wanke, Rüdiger; Wolf, Eckhard; Arnold, Georg J

2016-09-16

Duchenne muscular dystrophy (DMD) is caused by genetic deficiency of dystrophin and characterized by massive structural and functional changes of skeletal muscle tissue, leading to terminal muscle failure. We recently generated a novel genetically engineered pig model reflecting pathological hallmarks of human DMD better than the widely used mdx mouse. To get insight into the hierarchy of molecular derangements during DMD progression, we performed a proteome analysis of biceps femoris muscle samples from 2-day-old and 3-month-old DMD and wild-type (WT) pigs. The extent of proteome changes in DMD vs. WT muscle increased markedly with age, reflecting progression of the pathological changes. In 3-month-old DMD muscle, proteins related to muscle repair such as vimentin, nestin, desmin and tenascin C were found to be increased, whereas a large number of respiratory chain proteins were decreased in abundance in DMD muscle, indicating serious disturbances in aerobic energy production and a reduction of functional muscle tissue. The combination of proteome data for fiber type specific myosin heavy chain proteins and immunohistochemistry showed preferential degeneration of fast-twitch fiber types in DMD muscle. The stage-specific proteome changes detected in this large animal model of clinically severe muscular dystrophy provide novel molecular readouts for future treatment trials.

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data.

PubMed

Peterson, Elena S; McCue, Lee Ann; Schrimpe-Rutledge, Alexandra C; Jensen, Jeffrey L; Walker, Hyunjoo; Kobold, Markus A; Webb, Samantha R; Payne, Samuel H; Ansong, Charles; Adkins, Joshua N; Cannon, William R; Webb-Robertson, Bobbie-Jo M

2012-04-05

The procedural aspects of genome sequencing and assembly have become relatively inexpensive, yet the full, accurate structural annotation of these genomes remains a challenge. Next-generation sequencing transcriptomics (RNA-Seq), global microarrays, and tandem mass spectrometry (MS/MS)-based proteomics have demonstrated immense value to genome curators as individual sources of information, however, integrating these data types to validate and improve structural annotation remains a major challenge. Current visual and statistical analytic tools are focused on a single data type, or existing software tools are retrofitted to analyze new data forms. We present Visual Exploration and Statistics to Promote Annotation (VESPA) is a new interactive visual analysis software tool focused on assisting scientists with the annotation of prokaryotic genomes though the integration of proteomics and transcriptomics data with current genome location coordinates. VESPA is a desktop Java™ application that integrates high-throughput proteomics data (peptide-centric) and transcriptomics (probe or RNA-Seq) data into a genomic context, all of which can be visualized at three levels of genomic resolution. Data is interrogated via searches linked to the genome visualizations to find regions with high likelihood of mis-annotation. Search results are linked to exports for further validation outside of VESPA or potential coding-regions can be analyzed concurrently with the software through interaction with BLAST. VESPA is demonstrated on two use cases (Yersinia pestis Pestoides F and Synechococcus sp. PCC 7002) to demonstrate the rapid manner in which mis-annotations can be found and explored in VESPA using either proteomics data alone, or in combination with transcriptomic data. VESPA is an interactive visual analytics tool that integrates high-throughput data into a genomic context to facilitate the discovery of structural mis-annotations in prokaryotic genomes. Data is evaluated via visual analysis across multiple levels of genomic resolution, linked searches and interaction with existing bioinformatics tools. We highlight the novel functionality of VESPA and core programming requirements for visualization of these large heterogeneous datasets for a client-side application. The software is freely available at https://www.biopilot.org/docs/Software/Vespa.php.

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data

PubMed Central

2012-01-01

Background The procedural aspects of genome sequencing and assembly have become relatively inexpensive, yet the full, accurate structural annotation of these genomes remains a challenge. Next-generation sequencing transcriptomics (RNA-Seq), global microarrays, and tandem mass spectrometry (MS/MS)-based proteomics have demonstrated immense value to genome curators as individual sources of information, however, integrating these data types to validate and improve structural annotation remains a major challenge. Current visual and statistical analytic tools are focused on a single data type, or existing software tools are retrofitted to analyze new data forms. We present Visual Exploration and Statistics to Promote Annotation (VESPA) is a new interactive visual analysis software tool focused on assisting scientists with the annotation of prokaryotic genomes though the integration of proteomics and transcriptomics data with current genome location coordinates. Results VESPA is a desktop Java™ application that integrates high-throughput proteomics data (peptide-centric) and transcriptomics (probe or RNA-Seq) data into a genomic context, all of which can be visualized at three levels of genomic resolution. Data is interrogated via searches linked to the genome visualizations to find regions with high likelihood of mis-annotation. Search results are linked to exports for further validation outside of VESPA or potential coding-regions can be analyzed concurrently with the software through interaction with BLAST. VESPA is demonstrated on two use cases (Yersinia pestis Pestoides F and Synechococcus sp. PCC 7002) to demonstrate the rapid manner in which mis-annotations can be found and explored in VESPA using either proteomics data alone, or in combination with transcriptomic data. Conclusions VESPA is an interactive visual analytics tool that integrates high-throughput data into a genomic context to facilitate the discovery of structural mis-annotations in prokaryotic genomes. Data is evaluated via visual analysis across multiple levels of genomic resolution, linked searches and interaction with existing bioinformatics tools. We highlight the novel functionality of VESPA and core programming requirements for visualization of these large heterogeneous datasets for a client-side application. The software is freely available at https://www.biopilot.org/docs/Software/Vespa.php. PMID:22480257

Epidemiology and outcomes of older patients admitted to Scottish intensive care units: a national database linkage study.

PubMed

Docherty, Annemarie; Lone, Nazir; Anderson, Niall; Walsh, Timothy

2015-02-26

As the general population ages and life expectancy increases, health-care use by elderly people increases, including intensive care. Rationing and variation of access are ethically and politically challenging. We aimed to characterise the population-based incidence of intensive care unit (ICU) admissions of elderly people in Scotland; compare ICU admission and mortality between elderly and younger populations; and compare treatment intensity between these groups. We extracted complete, national 6-year cohort Scottish ICU admissions (Jan 1, 2005, to Dec 31, 2010) from the Scottish Intensive Care Society Audit Group database, which we linked to hospital Scottish Morbidity Record (SMR01) and death records. Annual incidence of ICU admissions of people aged 80 years or older was standardised for sex and socioeconomic status to the standard Scottish population (≥80 years) 2005-10. We compared mortality of elderly and younger people (<65 years) using the log-rank test. During 2005-10, 47 779 people were admitted to ICU (4561 patients ≥80 years [9·5%, 35·0/10 000 population], 26 784 patients <65 years [56·1%, 13·2/10 000]). Incidence of ICU admissions of elderly people fell from 36·6/10 000 population (95%CI 34·0-39·2) in 2005 to 30·3/10 000 (28·0-32·5) in 2010. ICU mortality was higher in elderly than in younger people (26·4% vs 16·1%, p<0·0001) as was 6-year mortality (68·0% vs 34·5%, p<0·0001). 2110 (80%) of 2627 elderly survivors were discharged home (younger 92%, 19 221/20 902), with a further 373 (14·2%) given rehabilitation (younger 1063, 5·1%) (χ(2)=525, p<0·0001). Age was an independent predictor of mortality (odds ratio 1·46, 95% CI 1·23-1·73, p<0·0001) after adjustment for confounders. In the pneumonia subgroup (elderly 294, younger 2167), mean acute physiology scores were similar (17·0 [SD 6·4] vs 17·6 [6·6]), organ support was higher in the elderly patients (77·0% vs 68·1%, p<0·0001), and median ICU length of stay was lower (6 days [IQR 3-13] vs 8 [3-16], p<0·0001). This study has shown that, by contrast with previously published research, admission rates of elderly people in Scotland fell between 2005 and 2010. Only the fittest elderly individuals were admitted to ICU, where initially they received a higher intensity of treatment than did younger patients; however, duration of ICU stay was shorter. Mortality rates were high, and age was an independent predictor of mortality. Funding assistance for AD's MPH from Scottish Intensive Care Society, Scottish Society of Anaesthetists, Edinburgh Anaesthetics Research and Education Fund. Copyright © 2015 Elsevier Ltd. All rights reserved.

Simple preparation of plant epidermal tissue for laser microdissection and downstream quantitative proteome and carbohydrate analysis

PubMed Central

Falter, Christian; Ellinger, Dorothea; von Hülsen, Behrend; Heim, René; Voigt, Christian A.

2015-01-01

The outwardly directed cell wall and associated plasma membrane of epidermal cells represent the first layers of plant defense against intruding pathogens. Cell wall modifications and the formation of defense structures at sites of attempted pathogen penetration are decisive for plant defense. A precise isolation of these stress-induced structures would allow a specific analysis of regulatory mechanism and cell wall adaption. However, methods for large-scale epidermal tissue preparation from the model plant Arabidopsis thaliana, which would allow proteome and cell wall analysis of complete, laser-microdissected epidermal defense structures, have not been provided. We developed the adhesive tape – liquid cover glass technique (ACT) for simple leaf epidermis preparation from A. thaliana, which is also applicable on grass leaves. This method is compatible with subsequent staining techniques to visualize stress-related cell wall structures, which were precisely isolated from the epidermal tissue layer by laser microdissection (LM) coupled to laser pressure catapulting. We successfully demonstrated that these specific epidermal tissue samples could be used for quantitative downstream proteome and cell wall analysis. The development of the ACT for simple leaf epidermis preparation and the compatibility to LM and downstream quantitative analysis opens new possibilities in the precise examination of stress- and pathogen-related cell wall structures in epidermal cells. Because the developed tissue processing is also applicable on A. thaliana, well-established, model pathosystems that include the interaction with powdery mildews can be studied to determine principal regulatory mechanisms in plant–microbe interaction with their potential outreach into crop breeding. PMID:25870605

Simple preparation of plant epidermal tissue for laser microdissection and downstream quantitative proteome and carbohydrate analysis.

PubMed

Falter, Christian; Ellinger, Dorothea; von Hülsen, Behrend; Heim, René; Voigt, Christian A

2015-01-01

The outwardly directed cell wall and associated plasma membrane of epidermal cells represent the first layers of plant defense against intruding pathogens. Cell wall modifications and the formation of defense structures at sites of attempted pathogen penetration are decisive for plant defense. A precise isolation of these stress-induced structures would allow a specific analysis of regulatory mechanism and cell wall adaption. However, methods for large-scale epidermal tissue preparation from the model plant Arabidopsis thaliana, which would allow proteome and cell wall analysis of complete, laser-microdissected epidermal defense structures, have not been provided. We developed the adhesive tape - liquid cover glass technique (ACT) for simple leaf epidermis preparation from A. thaliana, which is also applicable on grass leaves. This method is compatible with subsequent staining techniques to visualize stress-related cell wall structures, which were precisely isolated from the epidermal tissue layer by laser microdissection (LM) coupled to laser pressure catapulting. We successfully demonstrated that these specific epidermal tissue samples could be used for quantitative downstream proteome and cell wall analysis. The development of the ACT for simple leaf epidermis preparation and the compatibility to LM and downstream quantitative analysis opens new possibilities in the precise examination of stress- and pathogen-related cell wall structures in epidermal cells. Because the developed tissue processing is also applicable on A. thaliana, well-established, model pathosystems that include the interaction with powdery mildews can be studied to determine principal regulatory mechanisms in plant-microbe interaction with their potential outreach into crop breeding.

Ethnic Variations in Liver- and Alcohol-Related Disease Hospitalisations and Mortality: The Scottish Health and Ethnicity Linkage Study.

PubMed

Bhala, Neeraj; Cézard, Genevieve; Ward, Hester J T; Bansal, Narinder; Bhopal, Raj

2016-09-01

Preventing alcohol-related harms, including those causing liver disease, is a public health priority in the UK, especially in Scotland, but the effects of ethnicity are not known. We assessed liver- and alcohol-related events (hospitalisations and deaths) in Scotland using self-reported measures of ethnicity. Linking Scottish NHS hospital admissions and mortality to the Scottish Census 2001, we explored ethnic differences in hospitalisations and mortality (2001-2010) of all liver diseases, alcoholic liver disease (ALD) and specific alcohol-related diseases (ARD). Risk ratios (RR) were calculated using Poisson regression with robust variance, by sex, adjusted for age, country of birth and the Scottish Index of Multiple Deprivation (SIMD) presented below. The White Scottish population was the standard reference population with 95% confidence intervals (CI) calculated to enable comparison (multiplied by 100 for results). For all liver diseases, Chinese had around 50% higher risks for men (RR 162; 95% CI 127-207) and women (141; 109-184), as did Other South Asian men (144; 104-201) and Pakistani women (140; 116-168). Lower risks for all liver diseases occurred in African origin men (42; 24-74), other White British men (72; 63-82) and women (80; 70-90) and other White women (80; 67-94). For ALD, White Irish had a 75% higher risk for men (175; 107-287). Other White British men had about a third lower risk of ALD (63; 50-78), as did Pakistani men (65; 42-99). For ARD, almost 2-fold higher risks existed for White Irish men (182; 161-206) and Any Mixed Background women (199; 152-261). Lower risks of ARD existed in Pakistani men (67; 55-80) and women (48; 33-70), and Chinese men (55; 41-73) and women (54; 32-90). Substantial variations by ethnicity exist for both alcohol-related and liver disease hospitalisations and deaths in Scotland: these exist in subgroups of both White and non-White populations and practical actions are required to ameliorate these differences. © The Author 2016. Medical Council on Alcohol and Oxford University Press. All rights reserved.

Differential proteomics study of platelets in asymptomatic constitutional macrothrombocytopenia: altered levels of cytoskeletal proteins.

PubMed

Karmakar, Shilpita; Saha, Sutapa; Banerjee, Debasis; Chakrabarti, Abhijit

2015-01-01

Harris platelet syndrome (HPS), also known as asymptomatic constitutional macrothrombocytopenia (ACMT), is an autosomal dominant platelet disorder characterized by mild-to-severe thrombocytopenia and giant platelets with normal platelet aggregation and absence of bleeding symptoms. We have attempted a comparative proteomics study for profiling of platelet proteins in healthy vs. pathological states to discover characteristic protein expression changes in macrothrombocytes and decipher the factors responsible for the functionally active yet morphologically distinct platelets. We have used 2-D gel-based protein separation techniques coupled with MALDI-ToF/ToF-based mass spectrometric identification and characterization of the proteins to investigate the differential proteome profiling of platelet proteins isolated from the peripheral blood samples of patients and normal volunteers. Our study revealed altered levels of actin-binding proteins such as myosin light chain, coactosin-like protein, actin-related protein 2/3 complex, and transgelin2 that hint toward the cytoskeletal changes necessary to maintain the structural and functional integrity of macrothrombocytes. We have also observed over expressed levels of peroxiredoxin2 that signifies the prevailing oxidative stress in these cells. Additionally, altered levels of protein disulfide isomerase and transthyretin provide insights into the measures adapted by the macrothrombocytes to maintain their normal functional activity. This first proteomics study of platelets from ACMT may provide an understanding of the structural stability and normal functioning of these platelets in spite of their large size. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Isolation and Proteomic Characterization of the Mouse Sperm Acrosomal Matrix*

PubMed Central

Guyonnet, Benoit; Zabet-Moghaddam, Masoud; SanFrancisco, Susan; Cornwall, Gail A.

2012-01-01

A critical step during fertilization is the sperm acrosome reaction in which the acrosome releases its contents allowing the spermatozoa to penetrate the egg investments. The sperm acrosomal contents are composed of both soluble material and an insoluble material called the acrosomal matrix (AM). The AM is thought to provide a stable structure from which associated proteins are differentially released during fertilization. Because of its important role during fertilization, efforts have been put toward isolating the AM for biochemical study and to date AM have been isolated from hamster, guinea pig, and bull spermatozoa. However, attempts to isolate AM from mouse spermatozoa, the species in which fertilization is well-studied, have been unsuccessful possibly because of the small size of the mouse sperm acrosome and/or its fusiform shape. Herein we describe a procedure for the isolation of the AM from caput and cauda mouse epididymal spermatozoa. We further carried out a proteomic analysis of the isolated AM from both sperm populations and identified 501 new proteins previously not detected by proteomics in mouse spermatozoa. A comparison of the AM proteome from caput and cauda spermatozoa showed that the AM undergoes maturational changes during epididymal transit similar to other sperm domains. Together, our studies suggest the AM to be a dynamic and functional structure carrying out a variety of biological processes as implied by the presence of a diverse group of proteins including proteases, chaperones, hydrolases, transporters, enzyme modulators, transferases, cytoskeletal proteins, and others. PMID:22707618

Evolutionary conservation of the polyproline II conformation surrounding intrinsically disordered phosphorylation sites.

PubMed

Elam, W Austin; Schrank, Travis P; Campagnolo, Andrew J; Hilser, Vincent J

2013-04-01

Intrinsically disordered (ID) proteins function in the absence of a unique stable structure and appear to challenge the classic structure-function paradigm. The extent to which ID proteins take advantage of subtle conformational biases to perform functions, and whether signals for such mechanism can be identified in proteome-wide studies is not well understood. Of particular interest is the polyproline II (PII) conformation, suggested to be highly populated in unfolded proteins. We experimentally determine a complete calorimetric propensity scale for the PII conformation. Projection of the scale into representative eukaryotic proteomes reveals significant PII bias in regions coding for ID proteins. Importantly, enrichment of PII in ID proteins, or protein segments, is also captured by other PII scales, indicating that this enrichment is robustly encoded and universally detectable regardless of the method of PII propensity determination. Gene ontology (GO) terms obtained using our PII scale and other scales demonstrate a consensus for molecular functions performed by high PII proteins across the proteome. Perhaps the most striking result of the GO analysis is conserved enrichment (P < 10(-8) ) of phosphorylation sites in high PII regions found by all PII scales. Subsequent conformational analysis reveals a phosphorylation-dependent modulation of PII, suggestive of a conserved "tunability" within these regions. In summary, the application of an experimentally determined polyproline II (PII) propensity scale to proteome-wide sequence analysis and gene ontology reveals an enrichment of PII bias near disordered phosphorylation sites that is conserved throughout eukaryotes. Copyright © 2013 The Protein Society.

Toxicological effects of benzo(a)pyrene, DDT and their mixture on the green mussel Perna viridis revealed by proteomic and metabolomic approaches.

PubMed

Song, Qinqin; Chen, Hao; Li, Yuhu; Zhou, Hailong; Han, Qian; Diao, Xiaoping

2016-02-01

Benzo(a)pyrene (BaP) and dichlorodiphenyltrichloroethane (DDT) are persistent organic pollutants and environmental estrogens (EEs) with known toxicity towards the green mussel, Perna viridis. In this study, the toxic effects of BaP (10 µg/L) and DDT (10 µg/L) and their mixture were assessed in green mussel gills with proteomic and metabolomic approaches. Metabolic responses indicated that BaP mainly caused disturbance in osmotic regulation by significantly decrease in branched chain amino acids, dimethylamine and dimethylglycine in gills of male green mussels after exposure for 7 days. DDT mainly caused disturbance in osmotic regulation and energy metabolism by differential alteration of betaine, dimethylamine, dimethylglycine, amino acids, and succinate in gills of male green mussels. However, the mixture of BaP and DDT didn't show obvious metabolite changes. Proteomic analysis showed different protein expression profiles between different treatment groups, which demonstrated that BaP, DDT and their mixture may have different modes of action. Proteomic responses revealed that BaP induced cell apoptosis, disturbance in protein digestion and energy metabolism in gills of green mussels, whereas DDT exposure altered proteins that were associated with oxidative stress, cytoskeleton and cell structure, protein digestion and energy metabolism. However, the mixture of BaP and DDT affected proteins related to the oxidative stress, cytoskeleton and cell structure, protein biosynthesis and modification, energy metabolism, growth and apoptosis. Copyright © 2015 Elsevier Ltd. All rights reserved.

Molecular Simulation-Based Structural Prediction of Protein Complexes in Mass Spectrometry: The Human Insulin Dimer

PubMed Central

Li, Jinyu; Rossetti, Giulia; Dreyer, Jens; Raugei, Simone; Ippoliti, Emiliano; Lüscher, Bernhard; Carloni, Paolo

2014-01-01

Protein electrospray ionization (ESI) mass spectrometry (MS)-based techniques are widely used to provide insight into structural proteomics under the assumption that non-covalent protein complexes being transferred into the gas phase preserve basically the same intermolecular interactions as in solution. Here we investigate the applicability of this assumption by extending our previous structural prediction protocol for single proteins in ESI-MS to protein complexes. We apply our protocol to the human insulin dimer (hIns2) as a test case. Our calculations reproduce the main charge and the collision cross section (CCS) measured in ESI-MS experiments. Molecular dynamics simulations for 0.075 ms show that the complex maximizes intermolecular non-bonded interactions relative to the structure in water, without affecting the cross section. The overall gas-phase structure of hIns2 does exhibit differences with the one in aqueous solution, not inferable from a comparison with calculated CCS. Hence, care should be exerted when interpreting ESI-MS proteomics data based solely on NMR and/or X-ray structural information. PMID:25210764

Bruno Braunerde und die Bodentypen - The German-speaking friends of the Scottish soil characters

NASA Astrophysics Data System (ADS)

Hofmann, Anett

2014-05-01

Cartoon figures of soil profiles with faces, legs, arms and funny names: the Scottish soil characters Rusty (Cambisol), Heather (Podzol), Pete (Histosol) and five others were developed at the James Hutton Institute in Aberdeen for outreach activities. They represent eight soil types that are common in Scotland. Recently they have become movie stars in an animated film, where they speak with a Scottish accent. The Scottish soil characters are a true soil science communication success story and it would be great if they had friends in many places to tell some stories from the underground in the respective native languages. This contribution will introduce the draft for 13 German-speaking soil characters that represent the most common soil types in Austria, Germany and Switzerland. Each name is a play on words with respect to German soil classification terms and serves as a mnemonic for typical characteristics of these soils. The 'hair' shows detailed vegetation and the context with common land use. For non-soil scientists the soil characters can be used as story-tellers, e.g. about their life (soil evolution), home (spatial distribution), job (function), fears (threats) and joys (best-practice land use, restoration). Because the International Year of Soil (2015) is an excellent opportunity for new outreach activities, the aim is to publish the German-speaking soil characters as a collaboration of the Austrian, German and Swiss Soil Science Societies. The soil characters could be used in print or online formats, and even - as can be seen in Aberdeen - as human-sized walking soil profiles.

Television viewing and other screen-based entertainment in relation to multiple socioeconomic status indicators and area deprivation: the Scottish Health Survey 2003.

PubMed

Stamatakis, E; Hillsdon, M; Mishra, G; Hamer, M; Marmot, M

2009-09-01

Sedentary behaviour (sitting) is detrimental to health, independently of participation in physical activity. Socioeconomic position (SEP) is known to relate strongly to physical activity participation but we know very little about how SEP relates to sedentary behaviour. This study aimed to assess the relationships between SEP, neighbourhood deprivation and an index of sedentary time. Cross-sectional study of a representative sample of 7940 Scottish adults who participated in the 2003 Scottish Health Survey, which collected information on SEP (household income, social class and education), neighbourhood deprivation (Scottish Index of Multiple Deprivation), television and other screen-based entertainment time, and physical activity. The three indicators of SEP and deprivation index were independently of each other associated with daily times of television and other screen-based entertainment, even after adjustment for occupational and leisure-time physical activity, health status, smoking, alcohol drinking, car ownership and body mass index: income p = 0.002; social class p<0.001; education p<0.001, deprivation p<0.001. Also, there was a strong cumulative effect of SEP (a composite scale where 0 = lowest, 9 = highest SEP position) with those in the lowest SEP spending an additional 109 minutes each day on screen-based entertainment compared to those in the highest socioeconomic position (p<0.001 for linear trend). Adverse socioeconomic position is associated with a cumulative increase in the time spent on screen-based entertainment. Reducing inequalities would be expected to reduce exposure to sedentary behaviours, such as excessive screen-based entertainment times, and therefore reduce the risk of chronic disease.

Fjordic Environments of Scotland: A National Inventory of Sedimentary Blue Carbon.

NASA Astrophysics Data System (ADS)

Smeaton, Craig; Austin, William; Davies, Althea; Baltzer, Agnes; Howe, John

2016-04-01

Coastal sediments potentially hold a significant store of carbon; yet there has been no comprehensive attempt to quantitatively determine the quantity of carbon in these stores. Using Scottish sea lochs (fjords) we have established a Holocene record of the quantity and type of carbon held within the sediment store of a typical Scottish sea loch. Through the use of both seismic geophysics and geochemical measurements we have developed a methodology to make first-order estimations of the carbon held with the sediment of sea lochs. This methodology was applied to four sea lochs with differing geographical locations, catchments, freshwater inputs to produce the first sedimentary Blue Carbon estimates. The resulting carbon inventories show clearly that these sea lochs hold a significant store of sedimentary carbon; for example, Loch Sunart in Argyll stores an estimated 26.88 ± 0.52 Mt C. A direct comparison of the organic carbon content per unit area suggest sea lochs have a greater OC storage potential between than Scottish peatlands on long, Holocene timescales (Loch Sunart = 0.234 Mt OC km-2; Peatland = 0.093 Mt OC km-2 (Chapman et al. 2009). The carbon values calculated for these sea lochs have been used to estimate the total carbon held within Scotland's 110 sea lochs and these up-scaled estimations are for the first time, reviewed in the context of Scotland's known terrestrial stores. Chapman, S. J., Bell, J., Donnelly, D. and Lilly, A.: Carbon stocks in Scottish peatlands, Soil Use Manag., 25(2), 105-112, doi:10.1111/j.1475-2743.2009.00219.x, 2009.

Health visitor or public health nurse? A Scottish study.

PubMed

Wilson, Susan

2006-09-01

The Scottish Executive and the National Health Service (NHS) have been consistently promoting 'public health nursing' as a new way forward in the community. In addition, since 2001 traditional health visitor and school nurse education programmes have been replaced by a single public health nurse training curriculum. However, many of the roles, responsibilities and job descriptions of clinical health visiting staff have remained unchanged within health board areas. This has led to apparent confusion among staff, both newly qualified and those already in post. This lack of clarity in policy and role prompted this research study, which set out to investigate the perceptions of the public health role of the health visitor within a health board area in Scotland. Initially, a review of the relevant literature was undertaken to provide in-depth background information on the topic, to enable a critical analysis of the current public health role of the health visitor. This analysis was further informed by obtaining qualitative and quantitative data via a questionnaire sent to 89 health visitors, to determine the attitudes and opinions of health visitors currently working within a Scottish health board area. Results from the study indicate that, despite the plethora of public health-related Scottish Executive publications and the changes in educational programmes, many health visitors still carry out what is perceived as a traditional role with mainly the under-five age group. The study also identified the need for clear direction in the public health role for health visitors, with many health visitors expressing a willingness to make changes to their current role.

Two tales of cardiovascular risks-middle-aged women living in Sweden and Scotland: a cross-sectional comparative study.

PubMed

Wennerholm, Carina; Bromley, Catherine; Johansson, AnnaKarin; Nilsson, Staffan; Frank, John; Faresjö, Tomas

2017-08-07

To compare cardiovascular risk factors as well as rates of cardiovascular diseases in middle-aged women from urban areas in Scotland and Sweden. Comparative cross-sectional study. Data from the general population in urban areas of Scotland and the general population in two major Swedish cities in southeast Sweden, south of Stockholm. Comparable data of middle-aged women (40-65 years) from the Scottish Health Survey (n=6250) and the Swedish QWIN study (n=741) were merged together into a new dataset (n=6991 participants). We compared middle-aged women in urban areas in Sweden and Scotland regarding risk factors for cardiovascular disease (CVD), CVD diagnosis, anthropometrics, psychological distress and lifestyle. In almost all measurements, there were significant differences between the countries, favouring the Swedish women. Scottish women demonstrated a higher frequency of alcohol consumption, smoking, obesity, low vegetable consumption, a sedentary lifestyle and also more psychological distress. For doctor-diagnosed coronary heart disease, there were also significant differences, with a higher prevalence among the Scottish women. This is one of the first studies that clearly shows that Scottish middle-aged women are particularly affected by a worse profile of CVD risks. The profound differences in CVD risk and outcome frequency in the two populations are likely to have arisen from differences in the two groups of women's social, cultural, political and economic environments. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Structural and metabolic transitions of C4 leaf development and differentiation defined by microscopy and quantitative proteomics in maize.

PubMed

Majeran, Wojciech; Friso, Giulia; Ponnala, Lalit; Connolly, Brian; Huang, Mingshu; Reidel, Edwin; Zhang, Cankui; Asakura, Yukari; Bhuiyan, Nazmul H; Sun, Qi; Turgeon, Robert; van Wijk, Klaas J

2010-11-01

C(4) grasses, such as maize (Zea mays), have high photosynthetic efficiency through combined biochemical and structural adaptations. C(4) photosynthesis is established along the developmental axis of the leaf blade, leading from an undifferentiated leaf base just above the ligule into highly specialized mesophyll cells (MCs) and bundle sheath cells (BSCs) at the tip. To resolve the kinetics of maize leaf development and C(4) differentiation and to obtain a systems-level understanding of maize leaf formation, the accumulation profiles of proteomes of the leaf and the isolated BSCs with their vascular bundle along the developmental gradient were determined using large-scale mass spectrometry. This was complemented by extensive qualitative and quantitative microscopy analysis of structural features (e.g., Kranz anatomy, plasmodesmata, cell wall, and organelles). More than 4300 proteins were identified and functionally annotated. Developmental protein accumulation profiles and hierarchical cluster analysis then determined the kinetics of organelle biogenesis, formation of cellular structures, metabolism, and coexpression patterns. Two main expression clusters were observed, each divided in subclusters, suggesting that a limited number of developmental regulatory networks organize concerted protein accumulation along the leaf gradient. The coexpression with BSC and MC markers provided strong candidates for further analysis of C(4) specialization, in particular transporters and biogenesis factors. Based on the integrated information, we describe five developmental transitions that provide a conceptual and practical template for further analysis. An online protein expression viewer is provided through the Plant Proteome Database.

Identification of methyllysine peptides binding to chromobox protein homolog 6 chromodomain in the human proteome.

PubMed

Li, Nan; Stein, Richard S L; He, Wei; Komives, Elizabeth; Wang, Wei

2013-10-01

Methylation is one of the important post-translational modifications that play critical roles in regulating protein functions. Proteomic identification of this post-translational modification and understanding how it affects protein activity remain great challenges. We tackled this problem from the aspect of methylation mediating protein-protein interaction. Using the chromodomain of human chromobox protein homolog 6 as a model system, we developed a systematic approach that integrates structure modeling, bioinformatics analysis, and peptide microarray experiments to identify lysine residues that are methylated and recognized by the chromodomain in the human proteome. Given the important role of chromobox protein homolog 6 as a reader of histone modifications, it was interesting to find that the majority of its interacting partners identified via this approach function in chromatin remodeling and transcriptional regulation. Our study not only illustrates a novel angle for identifying methyllysines on a proteome-wide scale and elucidating their potential roles in regulating protein function, but also suggests possible strategies for engineering the chromodomain-peptide interface to enhance the recognition of and manipulate the signal transduction mediated by such interactions.

Proteomic Analysis of the Arabidopsis Nucleolus Suggests Novel Nucleolar FunctionsD⃞

PubMed Central

Pendle, Alison F.; Clark, Gillian P.; Boon, Reinier; Lewandowska, Dominika; Lam, Yun Wah; Andersen, Jens; Mann, Matthias; Lamond, Angus I.; Brown, John W. S.; Shaw, Peter J.

2005-01-01

The eukaryotic nucleolus is involved in ribosome biogenesis and a wide range of other RNA metabolism and cellular functions. An important step in the functional analysis of the nucleolus is to determine the complement of proteins of this nuclear compartment. Here, we describe the first proteomic analysis of plant (Arabidopsis thaliana) nucleoli, in which we have identified 217 proteins. This allows a direct comparison of the proteomes of an important nuclear structure between two widely divergent species: human and Arabidopsis. The comparison identified many common proteins, plant-specific proteins, proteins of unknown function found in both proteomes, and proteins that were nucleolar in plants but nonnucleolar in human. Seventy-two proteins were expressed as GFP fusions and 87% showed nucleolar or nucleolar-associated localization. In a striking and unexpected finding, we have identified six components of the postsplicing exon-junction complex (EJC) involved in mRNA export and nonsense-mediated decay (NMD)/mRNA surveillance. This association was confirmed by GFP-fusion protein localization. These results raise the possibility that in plants, nucleoli may have additional functions in mRNA export or surveillance. PMID:15496452

The jmzQuantML programming interface and validator for the mzQuantML data standard.

PubMed

Qi, Da; Krishna, Ritesh; Jones, Andrew R

2014-03-01

The mzQuantML standard from the HUPO Proteomics Standards Initiative has recently been released, capturing quantitative data about peptides and proteins, following analysis of MS data. We present a Java application programming interface (API) for mzQuantML called jmzQuantML. The API provides robust bridges between Java classes and elements in mzQuantML files and allows random access to any part of the file. The API provides read and write capabilities, and is designed to be embedded in other software packages, enabling mzQuantML support to be added to proteomics software tools (http://code.google.com/p/jmzquantml/). The mzQuantML standard is designed around a multilevel validation system to ensure that files are structurally and semantically correct for different proteomics quantitative techniques. In this article, we also describe a Java software tool (http://code.google.com/p/mzquantml-validator/) for validating mzQuantML files, which is a formal part of the data standard. © 2014 The Authors. Proteomics published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

OralCard: a bioinformatic tool for the study of oral proteome.

PubMed

Arrais, Joel P; Rosa, Nuno; Melo, José; Coelho, Edgar D; Amaral, Diana; Correia, Maria José; Barros, Marlene; Oliveira, José Luís

2013-07-01

The molecular complexity of the human oral cavity can only be clarified through identification of components that participate within it. However current proteomic techniques produce high volumes of information that are dispersed over several online databases. Collecting all of this data and using an integrative approach capable of identifying unknown associations is still an unsolved problem. This is the main motivation for this work. We present the online bioinformatic tool OralCard, which comprises results from 55 manually curated articles reflecting the oral molecular ecosystem (OralPhysiOme). It comprises experimental information available from the oral proteome both of human (OralOme) and microbial origin (MicroOralOme) structured in protein, disease and organism. This tool is a key resource for researchers to understand the molecular foundations implicated in biology and disease mechanisms of the oral cavity. The usefulness of this tool is illustrated with the analysis of the oral proteome associated with diabetes melitus type 2. OralCard is available at http://bioinformatics.ua.pt/oralcard. Copyright © 2013 Elsevier Ltd. All rights reserved.

Plant membrane proteomics.

PubMed

Ephritikhine, Geneviève; Ferro, Myriam; Rolland, Norbert

2004-12-01

Plant membrane proteins are involved in many different functions according to their location in the cell. For instance, the chloroplast has two membrane systems, thylakoids and envelope, with specialized membrane proteins for photosynthesis and metabolite and ion transporters, respectively. Although recent advances in sample preparation and analytical techniques have been achieved for the study of membrane proteins, the characterization of these proteins, especially the hydrophobic ones, is still challenging. The present review highlights recent advances in methodologies for identification of plant membrane proteins from purified subcellular structures. The interest of combining several complementary extraction procedures to take into account specific features of membrane proteins is discussed in the light of recent proteomics data, notably for chloroplast envelope, mitochondrial membranes and plasma membrane from Arabidopsis. These examples also illustrate how, on one hand, proteomics can feed bioinformatics for a better definition of prediction tools and, on the other hand, although prediction tools are not 100% reliable, they can give valuable information for biological investigations. In particular, membrane proteomics brings new insights over plant membrane systems, on both the membrane compartment where proteins are working and their putative cellular function.

Homicide and affective disorder.

PubMed

White, T

2004-04-01

The background, offence characteristics and psychiatric diagnosis were reviewed of 115 referrals of offenders charged with homicide made by procurators fiscal to the State Hospital, Carstairs, Scotland's only special secure hospital. A retrospective casenote review was performed using a structured questionnaire. A higher percentage of mental illness and substance misuse (11% and 40%) was recorded than that reported by Gillies in 1976. The results are discussed in the context of comparable studies and, in particular, the National Confidential Inquiry into Suicide and Homicide by People with Mental Illness and the Discussion Paper on Insanity and Diminished Responsibility published by the Scottish Law Commission.

Population Structure of Sclerotinia subarctica and Sclerotinia sclerotiorum in England, Scotland and Norway

PubMed Central

Clarkson, John P.; Warmington, Rachel J.; Walley, Peter G.; Denton-Giles, Matthew; Barbetti, Martin J.; Brodal, Guro; Nordskog, Berit

2017-01-01

Sclerotinia species are important fungal pathogens of a wide range of crops and wild host plants. While the biology and population structure of Sclerotinia sclerotiorum has been well-studied, little information is available for the related species S. subarctica. In this study, Sclerotinia isolates were collected from different crop plants and the wild host Ranuculus ficaria (meadow buttercup) in England, Scotland, and Norway to determine the incidence of Sclerotinia subarctica and examine the population structure of this pathogen for the first time. Incidence was very low in England, comprising only 4.3% of isolates while moderate and high incidence of S. subarctica was identified in Scotland and Norway, comprising 18.3 and 48.0% of isolates respectively. Characterization with eight microsatellite markers identified 75 haplotypes within a total of 157 isolates over the three countries with a few haplotypes in Scotland and Norway sampled at a higher frequency than the rest across multiple locations and host plants. In total, eight microsatellite haplotypes were shared between Scotland and Norway while none were shared with England. Bayesian and principal component analyses revealed common ancestry and clustering of Scottish and Norwegian S. subarctica isolates while English isolates were assigned to a separate population cluster and exhibited low diversity indicative of isolation. Population structure was also examined for S. sclerotiorum isolates from England, Scotland, Norway, and Australia using microsatellite data, including some from a previous study in England. In total, 484 haplotypes were identified within 800 S. sclerotiorum isolates with just 15 shared between England and Scotland and none shared between any other countries. Bayesian and principal component analyses revealed a common ancestry and clustering of the English and Scottish isolates while Norwegian and Australian isolates were assigned to separate clusters. Furthermore, sequencing part of the intergenic spacer (IGS) region of the rRNA gene resulted in 26 IGS haplotypes within 870 S. sclerotiorum isolates, nine of which had not been previously identified and two of which were also widely distributed across different countries. S. subarctica therefore has a multiclonal population structure similar to S. sclerotiorum, but has a different ancestry and distribution across England, Scotland, and Norway. PMID:28421039

An Awful and Impressive Spectacle: Crime Scene Executions in Scotland, 1801-1841

PubMed Central

Bennett, Rachel

2018-01-01

Early nineteenth-century Britain witnessed rising numbers of offenders facing capital punishment and a plethora of legal and public discourse debating the criminal justice system. This article will examine a distinct Scottish response to the problem in the form of crime scene executions. By the turn of the nineteenth century it had long been the established practice of the Scottish courts to order that capitally convicted offenders would be executed at an established ‘common place’. However, between 1801 and 1841, the decision was taken to execute 37 offenders at the scene of their crimes. This article argues that in the face of an unprecedented number of offenders facing the hangman’s noose the Scottish judges chose to exercise this penal option which had not been used to a similar extent since the mid-eighteenth century. In turn these events had a multiplicity of impact and provoked responses ranging from a morbid curiosity to witness the spectacle to anxiety and outright disdain at its intrusion into areas previously unsullied by the last punishment of the law. PMID:29780278

Scotland's Centre of Expertise for Waters - helping address Scotland's water policy challenges

NASA Astrophysics Data System (ADS)

MacDonald, Jannette; Morris, Sue; Hastings, Emily; Ferrier, Bob

2014-05-01

CREW connects water research and policy in Scotland. We deliver easily accessible research and expert opinion to support Scottish Government and its delivery partners in the development and implementation of water policy in Scotland. The main policy areas include the Water Framework Directive, Flooding Directive, and Scotland's Hydro Nation Strategy with links to cross cutting policies such as those relating to agriculture and climate change. CREW is unique in its demand-driven and free service for policy makers and practitioners, managing the engagement between scientists, policy makers and practitioners to work effectively across this interface. CREW aims are to; • deliver timely and accurate advice • coordinate and fund research, analysis and interpretation • stimulate innovative and proactive thinking • develop and implement a programme of knowledge exchange • develop the networks and skills of researchers, policy makers and practitioners to make best use of available science leading to improved environmental, social and economic outcomes for all CREW is a partnership between the James Hutton Institute and Scottish Universities, funded by the Scottish Government. http://www.crew.ac.uk/home

An evaluation of various methods of treatment for Legg-Calvé-Perthes disease.

PubMed

Wang, L; Bowen, J R; Puniak, M A; Guille, J T; Glutting, J

1995-05-01

An analysis of 5 methods of treatment for Legg-Calvé-Perthes disease was done on 124 patients with 141 affected hips. Before treatment, all groups were statistically similar concerning initial Mose measurement, age at onset of the disease, gender, and Catterall class. Treatments included the Scottish Rite orthosis (41 hips), nonweight bearing and exercises (41 hips), Petrie cast (29 hips), femoral varus osteotomy (15 hips), or Salter osteotomy (15 hips). Hips treated by the Scottish Rite orthosis had a significantly worse Mose measurement across time interaction (repeated measures analysis of variance, post hoc analyses, p < 0.05). For the other 4 treatment methods, there was no statistically different change. At followup, the Mose measurements for hips treated with the Scottish Rite orthosis were significantly worse than those for hips treated by nonweight bearing and exercises, Petrie cast, varus osteotomy, or Salter osteotomy (repeated measures analysis of variance, post hoc analyses, p < 0.05). There was, however, no significant difference in the distribution of hips according to the Stulberg et al classification at the last followup.

Aspiration, Agency, and the Production of New Selves in a Scottish New Town, c.1947-c.2016.

PubMed

Abrams, Lynn; Hazley, Barry; Wright, Valerie; Kearns, Ade

2018-05-30

Narratives of deindustrialization, urban decline and failing public housing and the negative outcomes associated with these processes dominate accounts of post-war Scotland, bolstering the interpretation of Scottish exceptionalism in a British context. Within these accounts working people appear as victims of powerful and long-term external forces suffering sustained and ongoing deleterious vulnerabilities in terms of employment, health, and housing. This article challenges this picture by focusing on the first Scottish new town which made space for working people's aspiration and new models of the self manifested in new lifestyles and social relations. Drawing on archival data and oral history interviews, we identify how elective relocation fostered and enabled new forms of identity predicated upon new housing, new social relations, and lifestyle opportunities focused on the family and home and elective social networks no longer determined by traditional class and gender expectations. These findings permit an intervention in the historical debates on post-war housing and social change which go beyond the materialistic experience to deeper and affective dimensions of the new town self.

Income, Wealth and Health Inequalities - A Scottish Social Justice Perspective.

PubMed

Molony, Elspeth; Duncan, Christine

2016-01-01

This paper considers health inequalities through a social justice perspective. The authors draw on a variety of existing sources of evidence, including experiential, scientific and contextual knowledge. The authors work with NHS Health Scotland, a national Health Board working to reduce health inequalities and improve health. Working closely with the Scottish Government and with a variety of stakeholders across different sectors, NHS Health Scotland's vision for a fairer, healthier Scotland is founded on the principles of social justice. The paper takes social justice as the starting point and explores what it means for two interlinked paradigms of social injustice-health inequality and income inequality. Utilising the wealth of evidence synthesised by NHS Health Scotland as well as drawing on the writings and evidence of philosophers, epidemiologists, the Scottish Government and international bodies, the authors explore the links between income and wealth inequality, social justice, the right to health and health inequalities. The paper ends by considering the extent to which there is appetite for social change in Scotland by considering the attitudes of the people of Scotland and of Britain to poverty, inequality and welfare.

Trends in bullying victimization in Scottish adolescents 1994-2014: changing associations with mental well-being.

PubMed

Cosma, Alina; Whitehead, Ross; Neville, Fergus; Currie, Dorothy; Inchley, Jo

2017-07-01

Bullying victimization among schoolchildren is a major public health concern. This paper aims to analyse the changing associations over two decades between bullying victimization and mental well-being in a representative Scottish schoolchildren sample. Data were collected in six rounds of the cross-sectional Health Behaviour in School-aged Children study in Scotland, with 42,312 adolescents (aged 11, 13 and 15 years). Logistic and linear regressions were used to examine changes in the association between bullying victimization and mental well-being. The prevalence of bullying victimization rates in Scotland increased between 1994 and 2014 for most age-gender groups, apart from 13-year-old boys and 15-year-old girls. Over time, female victims reported less confidence and happiness and more psychological complaints than their non-bullied counterparts. This worsening effect over time was not observed in boys. Overall, our evidence indicates that the associations between bullying victimization and poor mental well-being strengthened overtime for bullied girls. This finding might partly explain the observed deterioration in mental health indicators among Scottish adolescent girls.

Screening mammography uptake within Australia and Scotland in rural and urban populations

PubMed Central

Leung, Janni; Macleod, Catriona; McLaughlin, Deirdre; Woods, Laura M.; Henderson, Robert; Watson, Angus; Kyle, Richard G.; Hubbard, Gill; Mullen, Russell; Atherton, Iain

2015-01-01

Objective To test the hypothesis that rural populations had lower uptake of screening mammography than urban populations in the Scottish and Australian setting. Method Scottish data are based upon information from the Scottish Breast Screening Programme Information System describing uptake among women residing within the NHS Highland Health Board area who were invited to attend for screening during the 2008 to 2010 round (N = 27,416). Australian data were drawn from the 2010 survey of the 1946–51 cohort of the Australian Longitudinal Study on Women's Health (N = 9890 women). Results Contrary to our hypothesis, results indicated that women living in rural areas were not less likely to attend for screening mammography compared to women living in urban areas in both Scotland (OR for rural = 1.17, 95% CI = 1.06–1.29) and Australia (OR for rural = 1.15, 95% CI = 1.01–1.31). Conclusions The absence of rural–urban differences in attendance at screening mammography demonstrates that rurality is not necessarily an insurmountable barrier to screening mammography. PMID:26844118

Screening mammography uptake within Australia and Scotland in rural and urban populations.

PubMed

Leung, Janni; Macleod, Catriona; McLaughlin, Deirdre; Woods, Laura M; Henderson, Robert; Watson, Angus; Kyle, Richard G; Hubbard, Gill; Mullen, Russell; Atherton, Iain

2015-01-01

To test the hypothesis that rural populations had lower uptake of screening mammography than urban populations in the Scottish and Australian setting. Scottish data are based upon information from the Scottish Breast Screening Programme Information System describing uptake among women residing within the NHS Highland Health Board area who were invited to attend for screening during the 2008 to 2010 round (N = 27,416). Australian data were drawn from the 2010 survey of the 1946-51 cohort of the Australian Longitudinal Study on Women's Health (N = 9890 women). Contrary to our hypothesis, results indicated that women living in rural areas were not less likely to attend for screening mammography compared to women living in urban areas in both Scotland (OR for rural = 1.17, 95% CI = 1.06-1.29) and Australia (OR for rural = 1.15, 95% CI = 1.01-1.31). The absence of rural-urban differences in attendance at screening mammography demonstrates that rurality is not necessarily an insurmountable barrier to screening mammography.

Income, Wealth and Health Inequalities — A Scottish Social Justice Perspective

PubMed Central

Molony, Elspeth; Duncan, Christine

2016-01-01

This paper considers health inequalities through a social justice perspective. The authors draw on a variety of existing sources of evidence, including experiential, scientific and contextual knowledge. The authors work with NHS Health Scotland, a national Health Board working to reduce health inequalities and improve health. Working closely with the Scottish Government and with a variety of stakeholders across different sectors, NHS Health Scotland's vision for a fairer, healthier Scotland is founded on the principles of social justice. The paper takes social justice as the starting point and explores what it means for two interlinked paradigms of social injustice—health inequality and income inequality. Utilising the wealth of evidence synthesised by NHS Health Scotland as well as drawing on the writings and evidence of philosophers, epidemiologists, the Scottish Government and international bodies, the authors explore the links between income and wealth inequality, social justice, the right to health and health inequalities. The paper ends by considering the extent to which there is appetite for social change in Scotland by considering the attitudes of the people of Scotland and of Britain to poverty, inequality and welfare. PMID:29546160

Mapping of Proteomic Composition on the Surfaces of Bacillus spores by Atomic Force Microscopy-based Immunolabeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Plomp, M; Malkin, A J

2008-06-02

Atomic force microscopy provides a unique capability to image high-resolution architecture and structural dynamics of pathogens (e.g. viruses, bacteria and bacterial spores) at near molecular resolution in native conditions. Further development of atomic force microscopy in order to enable the correlation of pathogen protein surface structures with specific gene products is essential to understand the mechanisms of the pathogen life cycle. We have applied an AFM-based immunolabeling technique for the proteomic mapping of macromolecular structures through the visualization of the binding of antibodies, conjugated with nanogold particles, to specific epitopes on Bacillus spore surfaces. This information is generated while simultaneouslymore » acquiring the surface morphology of the pathogen. The immunospecificity of this labeling method was established through the utilization of specific polyclonal and monoclonal antibodies that target spore coat and exosporium epitopes of Bacillus atrophaeus and Bacillus anthracis spores.« less

Complete fold annotation of the human proteome using a novel structural feature space.

PubMed

Middleton, Sarah A; Illuminati, Joseph; Kim, Junhyong

2017-04-13

Recognition of protein structural fold is the starting point for many structure prediction tools and protein function inference. Fold prediction is computationally demanding and recognizing novel folds is difficult such that the majority of proteins have not been annotated for fold classification. Here we describe a new machine learning approach using a novel feature space that can be used for accurate recognition of all 1,221 currently known folds and inference of unknown novel folds. We show that our method achieves better than 94% accuracy even when many folds have only one training example. We demonstrate the utility of this method by predicting the folds of 34,330 human protein domains and showing that these predictions can yield useful insights into potential biological function, such as prediction of RNA-binding ability. Our method can be applied to de novo fold prediction of entire proteomes and identify candidate novel fold families.

Complete fold annotation of the human proteome using a novel structural feature space

PubMed Central

Middleton, Sarah A.; Illuminati, Joseph; Kim, Junhyong

2017-01-01

Recognition of protein structural fold is the starting point for many structure prediction tools and protein function inference. Fold prediction is computationally demanding and recognizing novel folds is difficult such that the majority of proteins have not been annotated for fold classification. Here we describe a new machine learning approach using a novel feature space that can be used for accurate recognition of all 1,221 currently known folds and inference of unknown novel folds. We show that our method achieves better than 94% accuracy even when many folds have only one training example. We demonstrate the utility of this method by predicting the folds of 34,330 human protein domains and showing that these predictions can yield useful insights into potential biological function, such as prediction of RNA-binding ability. Our method can be applied to de novo fold prediction of entire proteomes and identify candidate novel fold families. PMID:28406174

Chemical Proteomics and Structural Biology Define EPHA2 Inhibition by Clinical Kinase Drugs.

PubMed

Heinzlmeir, Stephanie; Kudlinzki, Denis; Sreeramulu, Sridhar; Klaeger, Susan; Gande, Santosh Lakshmi; Linhard, Verena; Wilhelm, Mathias; Qiao, Huichao; Helm, Dominic; Ruprecht, Benjamin; Saxena, Krishna; Médard, Guillaume; Schwalbe, Harald; Kuster, Bernhard

2016-12-16

The receptor tyrosine kinase EPHA2 (Ephrin type-A receptor 2) plays important roles in oncogenesis, metastasis, and treatment resistance, yet therapeutic targeting, drug discovery, or investigation of EPHA2 biology is hampered by the lack of appropriate inhibitors and structural information. Here, we used chemical proteomics to survey 235 clinical kinase inhibitors for their kinase selectivity and identified 24 drugs with submicromolar affinities for EPHA2. NMR-based conformational dynamics together with nine new cocrystal structures delineated drug-EPHA2 interactions in full detail. The combination of selectivity profiling, structure determination, and kinome wide sequence alignment allowed the development of a classification system in which amino acids in the drug binding site of EPHA2 are categorized into key, scaffold, potency, and selectivity residues. This scheme should be generally applicable in kinase drug discovery, and we anticipate that the provided information will greatly facilitate the development of selective EPHA2 inhibitors in particular and the repurposing of clinical kinase inhibitors in general.

Crystal Structure and Proteomics Analysis of Empty Virus-like Particles of Cowpea Mosaic Virus

PubMed Central

Huynh, Nhung T.; Hesketh, Emma L.; Saxena, Pooja; Meshcheriakova, Yulia; Ku, You-Chan; Hoang, Linh T.; Johnson, John E.; Ranson, Neil A.; Lomonossoff, George P.; Reddy, Vijay S.

2016-01-01

SUMMARY Empty virus-like particles (eVLPs) of Cowpea mosaic virus (CPMV) are currently being utilized as reagents in various biomedical and nanotechnology applications. Here, we report the crystal structure of CPMV eVLPs determined using X-ray crystallography at 2.3 Å resolution and compare it with previously reported cryo-electron microscopy (cryo-EM) of eVLPs and virion crystal structures. Although the X-ray and cryo-EM structures of eVLPs are mostly similar, there exist significant differences at the C terminus of the small (S) subunit. The intact C terminus of the S subunit plays a critical role in enabling the efficient assembly of CPMV virions and eVLPs, but undergoes proteolysis after particle formation. In addition, we report the results of mass spectrometry-based proteomics analysis of coat protein subunits from CPMV eVLPs and virions that identify the C termini of S subunits undergo proteolytic cleavages at multiple sites instead of a single cleavage site as previously observed. PMID:27021160

Proteome-level interplay between folding and aggregation propensities of proteins.

PubMed

Tartaglia, Gian Gaetano; Vendruscolo, Michele

2010-10-08

With the advent of proteomics, there is an increasing need of tools for predicting the properties of large numbers of proteins by using the information provided by their amino acid sequences, even in the absence of the knowledge of their structures. One of the most important types of predictions concerns whether proteins will fold or aggregate. Here, we study the competition between these two processes by analyzing the relationship between the folding and aggregation propensity profiles for the human and Escherichia coli proteomes. These profiles are calculated, respectively, using the CamFold method, which we introduce in this work, and the Zyggregator method. Our results indicate that the kinetic behavior of proteins is, to a large extent, determined by the interplay between regions of low folding and high aggregation propensities. Copyright © 2010. Published by Elsevier Ltd.

Novel remodeling of the mouse heart mitochondrial proteome in response to acute insulin stimulation

PubMed Central

Pedersen, Brian A; Yazdi, Puya G; Taylor, Jared F; Khattab, Omar S; Chen, Yu-Han; Chen, Yumay; Wang, Ping H

2015-01-01

Mitochondrial dysfunction contributes to the pathophysiology of diabetic cardiomyopathy. The aim of this study was to investigate the acute changes in the mitochondrial proteome in response to insulin stimulation. Cardiac mitochondria from C57BL/6 mice after insulin stimulation were analyzed using two-dimensional fluorescence difference gel electrophoresis. MALDI-TOF MS/MS was utilized to identify differences. Two enzymes involved in metabolism and four structural proteins were identified. Succinyl-CoA ligase [ADP forming] subunit beta was identified as one of the differentially regulated proteins. Upon insulin stimulation, a relatively more acidic isoform of this protein was increased by 53% and its functional activity was decreased by ∼32%. This proteomic remodeling in response to insulin stimulation may play an important role in the normal and diabetic heart. PMID:26610654

Architecture Mapping of the Inner Mitochondrial Membrane Proteome by Chemical Tools in Live Cells.

PubMed

Lee, Song-Yi; Kang, Myeong-Gyun; Shin, Sanghee; Kwak, Chulhwan; Kwon, Taejoon; Seo, Jeong Kon; Kim, Jong-Seo; Rhee, Hyun-Woo

2017-03-15

The inner mitochondrial membrane (IMM) proteome plays a central role in maintaining mitochondrial physiology and cellular metabolism. Various important biochemical reactions such as oxidative phosphorylation, metabolite production, and mitochondrial biogenesis are conducted by the IMM proteome, and mitochondria-targeted therapeutics have been developed for IMM proteins, which is deeply related for various human metabolic diseases including cancer and neurodegenerative diseases. However, the membrane topology of the IMM proteome remains largely unclear because of the lack of methods to evaluate it in live cells in a high-throughput manner. In this article, we reveal the in vivo topological direction of 135 IMM proteins, using an in situ-generated radical probe with genetically targeted peroxidase (APEX). Owing to the short lifetime of phenoxyl radicals generated in situ by submitochondrial targeted APEX and the impermeability of the IMM to small molecules, the solvent-exposed tyrosine residues of both the matrix and intermembrane space (IMS) sides of IMM proteins were exclusively labeled with the radical probe in live cells by Matrix-APEX and IMS-APEX, respectively and identified by mass spectrometry. From this analysis, we confirmed 58 IMM protein topologies and we could determine the topological direction of 77 IMM proteins whose topology at the IMM has not been fully characterized. We also found several IMM proteins (e.g., LETM1 and OXA1) whose topological information should be revised on the basis of our results. Overall, our identification of structural information on the mitochondrial inner-membrane proteome can provide valuable insights for the architecture and connectome of the IMM proteome in live cells.

Improving Outcomes through Transformational Health and Social Care Integration - The Scottish Experience.

PubMed

Hendry, Anne; Taylor, Alison; Mercer, Stewart; Knight, Peter

2016-01-01

The Scottish Parliament recently passed legislation on integrating healthcare and social care to improve the quality and outcomes of care and support for people with multiple and complex needs across Scotland. This ambitious legislation provides a national framework to accelerate progress in person-centred and integrated care and support for the growing number of people who have multiple physical and mental health conditions and complex needs. Additional investment and improvement capacity is helping to commission support and services that are designed and delivered with people in local communities and in partnership with housing, community, voluntary and independent sectors.

VESPA: Software to Facilitate Genomic Annotation of Prokaryotic Organisms Through Integration of Proteomic and Transcriptomic Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peterson, Elena S.; McCue, Lee Ann; Rutledge, Alexandra C.

2012-04-25

Visual Exploration and Statistics to Promote Annotation (VESPA) is an interactive visual analysis software tool that facilitates the discovery of structural mis-annotations in prokaryotic genomes. VESPA integrates high-throughput peptide-centric proteomics data and oligo-centric or RNA-Seq transcriptomics data into a genomic context. The data may be interrogated via visual analysis across multiple levels of genomic resolution, linked searches, exports and interaction with BLAST to rapidly identify location of interest within the genome and evaluate potential mis-annotations.

Dodecyl Maltopyranoside Enabled Purification of Active Human GABA Type A Receptors for Deep and Direct Proteomic Sequencing*

PubMed Central

Zhang, Xi; Miller, Keith W.

2015-01-01

The challenge in high-quality membrane proteomics is all about sample preparation prior to HPLC, and the cell-to-protein step poses a long-standing bottleneck. Traditional protein extraction methods apply ionic or poly-disperse detergents, harsh denaturation, and repeated protein/peptide precipitation/resolubilization afterward, but suffer low yield, low reproducibility, and low sequence coverage. Contrary to attempts to subdue, we resolved this challenge by providing proteins nature-and-activity-promoting conditions throughout preparation. Using 285-kDa hetero-pentameric human GABA type A receptor overexpressed in HEK293 as a model, we describe a n-dodecyl-β-d-maltopyranoside/cholesteryl hemisuccinate (DDM/CHS)-based affinity purification method, that produced active receptors, supported protease activity, and allowed high performance with both in-gel and direct gel-free proteomic analyses—without detergent removal. Unlike conventional belief that detergents must be removed before HPLC MS, the high-purity low-dose nonionic detergent DDM did not interfere with peptides, and obviated removal or desalting. Sonication or dropwise addition of detergent robustly solubilized over 90% of membrane pellets. The purification conditions were comparable to those applied in successful crystallizations of most membrane proteins. These results enabled streamlined proteomics of human synaptic membrane proteins, and more importantly, allowed directly coupling proteomics with crystallography to characterize both static and dynamic structures of membrane proteins in crystallization pipelines. PMID:25473089

Proteomic Approaches to Quantify Cysteine Reversible Modifications in Aging and Neurodegenerative Diseases

PubMed Central

Gu, Liqing; Robinson, Renã A. S.

2016-01-01

Cysteine is a highly reactive amino acid and is subject to a variety of reversible post-translational modifications (PTMs), including nitrosylation, glutathionylation, palmitoylation, as well as formation of sulfenic acid and disulfides. These modifications are not only involved in normal biological activities, such as enzymatic catalysis, redox signaling and cellular homeostasis, but can also be the result of oxidative damage. Especially in aging and neurodegenerative diseases, oxidative stress leads to aberrant cysteine oxidations that affect protein structure and function leading to neurodegeneration as well as other detrimental effects. Methods that can identify cysteine modifications by type, including the site of modification, as well as the relative stoichiometry of the modification can be very helpful for understanding the role of the thiol proteome and redox homeostasis in the context of disease. Cysteine reversible modifications however, are challenging to investigate as they are low abundant, diverse, and labile especially under endogenous conditions. Thanks to the development of redox proteomic approaches, large-scale quantification of cysteine reversible modifications is possible. These approaches cover a range of strategies to enrich, identify, and quantify cysteine reversible modifications from biological samples. This review will focus on nongel-based redox proteomics workflows that give quantitative information about cysteine PTMs and highlight how these strategies have been useful for investigating the redox thiol proteome in aging and neurodegenerative diseases. PMID:27666938

Combined analysis of transcriptome and proteome data as a tool for the identification of candidate biomarkers in renal cell carcinoma

PubMed Central

Seliger, Barbara; Dressler, Sven P.; Wang, Ena; Kellner, Roland; Recktenwald, Christian V.; Lottspeich, Friedrich; Marincola, Francesco M.; Baumgärtner, Maja; Atkins, Derek; Lichtenfels, Rudolf

2012-01-01

Results obtained from expression profilings of renal cell carcinoma using different “ome”-based approaches and comprehensive data analysis demonstrated that proteome-based technologies and cDNA microarray analyses complement each other during the discovery phase for disease-related candidate biomarkers. The integration of the respective data revealed the uniqueness and complementarities of the different technologies. While comparative cDNA microarray analyses though restricted to upregulated targets largely revealed genes involved in controlling gene/protein expression (19%) and signal transduction processes (13%), proteomics/PROTEOMEX-defined candidate biomarkers include enzymes of the cellular metabolism (36%), transport proteins (12%) and cell motility/structural molecules (10%). Candidate biomarkers defined by proteomics and PROTEOMEX are frequently shared, whereas the sharing rate between cDNA microarray and proteome-based profilings is limited. Putative candidate biomarkers provide insights into their cellular (dys)function and their diagnostic/prognostic value but still warrant further validation in larger patient numbers. Based on the fact that merely 3 candidate biomarkers were shared by all applied technologies, namely annexin A4, tubulin alpha-1A chain and ubiquitin carboxyl-terminal hydrolase L1 the analysis at a single hierarchical level of biological regulation seems to provide only limited results thus emphasizing the importance and benefit of performing rather combinatorial screenings which can complement the standard clinical predictors. PMID:19235166

An object model and database for functional genomics.

PubMed

Jones, Andrew; Hunt, Ela; Wastling, Jonathan M; Pizarro, Angel; Stoeckert, Christian J

2004-07-10

Large-scale functional genomics analysis is now feasible and presents significant challenges in data analysis, storage and querying. Data standards are required to enable the development of public data repositories and to improve data sharing. There is an established data format for microarrays (microarray gene expression markup language, MAGE-ML) and a draft standard for proteomics (PEDRo). We believe that all types of functional genomics experiments should be annotated in a consistent manner, and we hope to open up new ways of comparing multiple datasets used in functional genomics. We have created a functional genomics experiment object model (FGE-OM), developed from the microarray model, MAGE-OM and two models for proteomics, PEDRo and our own model (Gla-PSI-Glasgow Proposal for the Proteomics Standards Initiative). FGE-OM comprises three namespaces representing (i) the parts of the model common to all functional genomics experiments; (ii) microarray-specific components; and (iii) proteomics-specific components. We believe that FGE-OM should initiate discussion about the contents and structure of the next version of MAGE and the future of proteomics standards. A prototype database called RNA And Protein Abundance Database (RAPAD), based on FGE-OM, has been implemented and populated with data from microbial pathogenesis. FGE-OM and the RAPAD schema are available from http://www.gusdb.org/fge.html, along with a set of more detailed diagrams. RAPAD can be accessed by registration at the site.

Circulating protein synthesis rates reveal skeletal muscle proteome dynamics

PubMed Central

Shankaran, Mahalakshmi; King, Chelsea L.; Angel, Thomas E.; Holmes, William E.; Li, Kelvin W.; Colangelo, Marc; Price, John C.; Turner, Scott M.; Bell, Christopher; Hamilton, Karyn L.; Miller, Benjamin F.; Hellerstein, Marc K.

2015-01-01

Here, we have described and validated a strategy for monitoring skeletal muscle protein synthesis rates in rodents and humans over days or weeks from blood samples. We based this approach on label incorporation into proteins that are synthesized specifically in skeletal muscle and escape into the circulation. Heavy water labeling combined with sensitive tandem mass spectrometric analysis allowed integrated synthesis rates of proteins in muscle tissue across the proteome to be measured over several weeks. Fractional synthesis rate (FSR) of plasma creatine kinase M-type (CK-M) and carbonic anhydrase 3 (CA-3) in the blood, more than 90% of which is derived from skeletal muscle, correlated closely with FSR of CK-M, CA-3, and other proteins of various ontologies in skeletal muscle tissue in both rodents and humans. Protein synthesis rates across the muscle proteome generally changed in a coordinate manner in response to a sprint interval exercise training regimen in humans and to denervation or clenbuterol treatment in rodents. FSR of plasma CK-M and CA-3 revealed changes and interindividual differences in muscle tissue proteome dynamics. In human subjects, sprint interval training primarily stimulated synthesis of structural and glycolytic proteins. Together, our results indicate that this approach provides a virtual biopsy, sensitively revealing individualized changes in proteome-wide synthesis rates in skeletal muscle without a muscle biopsy. Accordingly, this approach has potential applications for the diagnosis, management, and treatment of muscle disorders. PMID:26657858

Comparative proteomics analysis of oral cancer cell lines: identification of cancer associated proteins

PubMed Central

2014-01-01

Background A limiting factor in performing proteomics analysis on cancerous cells is the difficulty in obtaining sufficient amounts of starting material. Cell lines can be used as a simplified model system for studying changes that accompany tumorigenesis. This study used two-dimensional gel electrophoresis (2DE) to compare the whole cell proteome of oral cancer cell lines vs normal cells in an attempt to identify cancer associated proteins. Results Three primary cell cultures of normal cells with a limited lifespan without hTERT immortalization have been successfully established. 2DE was used to compare the whole cell proteome of these cells with that of three oral cancer cell lines. Twenty four protein spots were found to have changed in abundance. MALDI TOF/TOF was then used to determine the identity of these proteins. Identified proteins were classified into seven functional categories – structural proteins, enzymes, regulatory proteins, chaperones and others. IPA core analysis predicted that 18 proteins were related to cancer with involvements in hyperplasia, metastasis, invasion, growth and tumorigenesis. The mRNA expressions of two proteins – 14-3-3 protein sigma and Stress-induced-phosphoprotein 1 – were found to correlate with the corresponding proteins’ abundance. Conclusions The outcome of this analysis demonstrated that a comparative study of whole cell proteome of cancer versus normal cell lines can be used to identify cancer associated proteins. PMID:24422745

Quantitative proteomics-based analysis supports a significant role of GTG proteins in regulation of ABA response in Arabidopsis roots.

PubMed

Alvarez, Sophie; Roy Choudhury, Swarup; Hicks, Leslie M; Pandey, Sona

2013-03-01

Abscisic acid (ABA) is proposed to be perceived by multiple receptors in plants. We have previously reported on the role of two GPCR-type G-proteins (GTG proteins) as plasma membrane-localized ABA receptors in Arabidopsis thaliana. However, due to the presence of multiple transmembrane domains, detailed structural and biochemical characterization of GTG proteins remains limited. Since ABA induces substantial changes in the proteome of plants, a labeling LC-based quantitative proteomics approach was applied to elucidate the global effects and possible downstream targets of GTG1/GTG2 proteins. Quantitative differences in protein abundance between wild-type and gtg1gtg2 were analyzed for evaluation of the effect of ABA on the root proteome and its dependence on the presence of functional GTG1/GTG2 proteins. The results presented in this study reveal the most comprehensive ABA-responsive root proteome reported to date in Arabidopsis. Notably, the majority of ABA-responsive proteins required the presence of GTG proteins, supporting their key role in ABA signaling. These observations were further confirmed by additional experiments. Overall, comparison of the ABA-dependent protein abundance changes in wild-type versus gtg1gtg2 provides clues to their possible links with some of the well-established effectors of the ABA signaling pathways and their role in mediating phytohormone cross-talk.

Fasting and refeeding induces changes in the mouse hepatic lipid droplet proteome.

PubMed

Kramer, David A; Quiroga, Ariel D; Lian, Jihong; Fahlman, Richard P; Lehner, Richard

2018-06-15

During fasting, the liver increases lipid storage as a mean to reserve and provide energy for vital cellular functions. After re-feeding, hepatocytes rapidly decrease the amount of triacylglycerol that is stored in lipid droplets (LDs), visible as the size of hepatic LDs significantly decreases after re-feeding. Little is known about the changes in the liver LD proteome that occur during the fasting/re-feeding transition. This study aimed to investigate the hepatic LD proteome in fasted and re-fed conditions in the mouse. Using label-free LC-MS/MS analysis the relative abundance of 817 proteins was determined in highly purified LDs. Comparative analysis for differential protein abundance with respect to feeding states revealed 130 with higher abundance in LDs from fasted mice and 31 in LDs from re-fed mice. Among proteins observed to have higher abundance on LDs in the fasted state we found perilipin-5, and several mitochondrial and peroxisomal marker proteins, supporting the role of LDs in the provision of substrates for fatty acid oxidation. Proteins of higher abundance upon re-feeding included several peroxisomal and mitochondrial marker proteins and expand our understanding of the dynamic nature of the hepatic LD proteome according to the energetic requirements of the cell. Proteomic investigations have been revealing the complexities and dynamics of cellular LDs from a variety of cell types. As these sub-cellular structures are truly dynamic in nature, our investigations reveal that simply the feeding state of an animal leads to significant changes to the protein composition of LDs and suggest a variety of dynamic interactions with other cellular organelles, such as the mitochondria and peroxisomes. As such, the experimental design for investigations of this cellular structure must consider this dynamic baseline. Lastly our analysis on global protein abundance has revealed the unforeseen high abundance of murine major urinary proteins associated with hepatic lipid droplets, which warrants further investigations. Crown Copyright © 2018. Published by Elsevier B.V. All rights reserved.

Proteome-wide Subcellular Topologies of E. coli Polypeptides Database (STEPdb)*

PubMed Central

Orfanoudaki, Georgia; Economou, Anastassios

2014-01-01

Cell compartmentalization serves both the isolation and the specialization of cell functions. After synthesis in the cytoplasm, over a third of all proteins are targeted to other subcellular compartments. Knowing how proteins are distributed within the cell and how they interact is a prerequisite for understanding it as a whole. Surface and secreted proteins are important pathogenicity determinants. Here we present the STEP database (STEPdb) that contains a comprehensive characterization of subcellular localization and topology of the complete proteome of Escherichia coli. Two widely used E. coli proteomes (K-12 and BL21) are presented organized into thirteen subcellular classes. STEPdb exploits the wealth of genetic, proteomic, biochemical, and functional information on protein localization, secretion, and targeting in E. coli, one of the best understood model organisms. Subcellular annotations were derived from a combination of bioinformatics prediction, proteomic, biochemical, functional, topological data and extensive literature re-examination that were refined through manual curation. Strong experimental support for the location of 1553 out of 4303 proteins was based on 426 articles and some experimental indications for another 526. Annotations were provided for another 320 proteins based on firm bioinformatic predictions. STEPdb is the first database that contains an extensive set of peripheral IM proteins (PIM proteins) and includes their graphical visualization into complexes, cellular functions, and interactions. It also summarizes all currently known protein export machineries of E. coli K-12 and pairs them, where available, with the secretory proteins that use them. It catalogs the Sec- and TAT-utilizing secretomes and summarizes their topological features such as signal peptides and transmembrane regions, transmembrane topologies and orientations. It also catalogs physicochemical and structural features that influence topology such as abundance, solubility, disorder, heat resistance, and structural domain families. Finally, STEPdb incorporates prediction tools for topology (TMHMM, SignalP, and Phobius) and disorder (IUPred) and implements the BLAST2STEP that performs protein homology searches against the STEPdb. PMID:25210196

A structured proteomic approach identifies 14-3-3Sigma as a novel and reliable protein biomarker in panel based differential diagnostics of liver tumors.

PubMed

Reis, Henning; Pütter, Carolin; Megger, Dominik A; Bracht, Thilo; Weber, Frank; Hoffmann, Andreas-C; Bertram, Stefanie; Wohlschläger, Jeremias; Hagemann, Sascha; Eisenacher, Martin; Scherag, André; Schlaak, Jörg F; Canbay, Ali; Meyer, Helmut E; Sitek, Barbara; Baba, Hideo A

2015-06-01

Hepatocellular carcinoma (HCC) is a major lethal cancer worldwide. Despite sophisticated diagnostic algorithms, the differential diagnosis of small liver nodules still is difficult. While imaging techniques have advanced, adjuvant protein-biomarkers as glypican3 (GPC3), glutamine-synthetase (GS) and heat-shock protein 70 (HSP70) have enhanced diagnostic accuracy. The aim was to further detect useful protein-biomarkers of HCC with a structured systematic approach using differential proteome techniques, bring the results to practical application and compare the diagnostic accuracy of the candidates with the established biomarkers. After label-free and gel-based proteomics (n=18 HCC/corresponding non-tumorous liver tissue (NTLT)) biomarker candidates were tested for diagnostic accuracy in immunohistochemical analyses (n=14 HCC/NTLT). Suitable candidates were further tested for consistency in comparison to known protein-biomarkers in HCC (n=78), hepatocellular adenoma (n=25; HCA), focal nodular hyperplasia (n=28; FNH) and cirrhosis (n=28). Of all protein-biomarkers, 14-3-3Sigma (14-3-3S) exhibited the most pronounced up-regulation (58.8×) in proteomics and superior diagnostic accuracy (73.0%) in the differentiation of HCC from non-tumorous hepatocytes also compared to established biomarkers as GPC3 (64.7%) and GS (45.4%). 14-3-3S was part of the best diagnostic three-biomarker panel (GPC3, HSP70, 14-3-3S) for the differentiation of HCC and HCA which is of most important significance. Exclusion of GS and inclusion of 14-3-3S in the panel (>1 marker positive) resulted in a profound increase in specificity (+44.0%) and accuracy (+11.0%) while sensitivity remained stable (96.0%). 14-3-3S is an interesting protein biomarker with the potential to further improve the accuracy of differential diagnostic process of hepatocellular tumors. This article is part of a Special Issue entitled: Medical Proteomics. Copyright © 2014 Elsevier B.V. All rights reserved.

Utilization of protein intrinsic disorder knowledge in structural proteomics

PubMed Central

Oldfield, Christopher J.; Xue, Bin; Van, Ya-Yue; Ulrich, Eldon L.; Markley, John L.; Dunker, A. Keith; Uversky, Vladimir N.

2014-01-01

Intrinsically disordered proteins (IDPs) and proteins with long disordered regions are highly abundant in various proteomes. Despite their lack of well-defined ordered structure, these proteins and regions are frequently involved in crucial biological processes. Although in recent years these proteins have attracted the attention of many researchers, IDPs represent a significant challenge for structural characterization since these proteins can impact many of the processes in the structure determination pipeline. Here we investigate the effects of IDPs on the structure determination process and the utility of disorder prediction in selecting and improving proteins for structural characterization. Examination of the extent of intrinsic disorder in existing crystal structures found that relatively few protein crystal structures contain extensive regions of intrinsic disorder. Although intrinsic disorder is not the only cause of crystallization failures and many structured proteins cannot be crystallized, filtering out highly disordered proteins from structure-determination target lists is still likely to be cost effective. Therefore it is desirable to avoid highly disordered proteins from structure-determination target lists and we show that disorder prediction can be applied effectively to enrich structure determination pipelines with proteins more likely to yield crystal structures. For structural investigation of specific proteins, disorder prediction can be used to improve targets for structure determination. Finally, a framework for considering intrinsic disorder in the structure determination pipeline is proposed. PMID:23232152

Recruitment, selection and retention of nursing and midwifery students in Scottish Universities.

PubMed

Rodgers, Sheila; Stenhouse, Rosie; McCreaddie, May; Small, Pauline

2013-11-01

High attrition rates from pre-registration nursing and midwifery programmes have been reported in both the UK and in other countries. A study was conducted to identify best practice in recruitment, selection and retention across Scottish Universities providing pre-registration programmes. A survey of all universities providing pre-registration programmes in Scotland was conducted. Semi-structured interviews were conducted with key personnel in each university. Documentary evidence was collected to supplement interview data and evidence recruitment, selection and retention practices. All universities in Scotland providing pre-registration nursing and/or midwifery programmes. All 10 identified universities agreed to take part and a total of 18 interviews were conducted. Semi-structured face to face and telephone interviews were conducted. Relevant documentary evidence was collected. All data were subject to thematic analysis. Universities are predominantly concerned with recruiting to the institution and not to the professions. Interviews are widely used, and are a requirement in the United Kingdom. However, there is no evidence base within the literature that they have predictive validity despite creating scales and scoring systems which are largely unvalidated. The study identified initiatives aimed at addressing attrition/retention, however most had not been evaluated often due to the multi-factorial nature of attrition/retention and difficulties with measurement. Recruitment selection and retention initiatives were rarely evaluated, and if so, adopted a relatively superficial approach. Evidence from existing studies to support practices was mostly weakly supportive or absent. The study highlights the need for a coordinated approach, supporting the development of a robust evidence base through the evaluation of local initiatives, and evaluation of new strategies. Evaluation strategies must take account of the local context to facilitate transferability of findings across different settings. Copyright © 2013 Elsevier Ltd. All rights reserved.

Tobacco Retail Environments and Social Inequalities in Individual-Level Smoking and Cessation Among Scottish Adults.

PubMed

Pearce, Jamie; Rind, Esther; Shortt, Niamh; Tisch, Catherine; Mitchell, Richard

2016-02-01

Many neighborhood characteristics may constrain or enable smoking. This study investigated whether the neighborhood tobacco retail environment was associated with individual-level smoking and cessation in Scottish adults, and whether inequalities in smoking status were related to tobacco retailing. Tobacco outlet density measures were developed for neighborhoods across Scotland using the September 2012 Scottish Tobacco Retailers Register. The outlet data were cleaned and geocoded (n = 10,161) using a Geographic Information System. Kernel density estimation was used to calculate an outlet density measure for each postcode. The kernel density estimation measures were then appended to data on individuals included in the 2008-2011 Scottish Health Surveys (n = 28,751 adults aged ≥16), via their postcode. Two-level logistic regression models examined whether neighborhood density of tobacco retailing was associated with current smoking status and smoking cessation and whether there were differences in the relationship between household income and smoking status, by tobacco outlet density. After adjustment for individual- and area-level confounders, compared to residents of areas with the lowest outlet densities, those living in areas with the highest outlet densities had a 6% higher chance of being a current smoker, and a 5% lower chance of being an ex-smoker. There was little evidence to suggest that inequalities in either current smoking or cessation were narrower in areas with lower availability of tobacco retailing. The findings suggest that residents of environments with a greater availability of tobacco outlets are more likely to start and/or sustain smoking, and less likely to quit. © The Author 2015. Published by Oxford University Press on behalf of the Society for Research on Nicotine and Tobacco. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Correlations of indoor second-hand smoking, household smoking rules, regional deprivation and children mental health: Scottish Health Survey, 2013.

PubMed

Shiue, Ivy

2015-07-01

It has been known that second-hand smoking and deprivation could cluster together affecting child health. However, little is known on the role of household smoking rules. Therefore, it was aimed to study the relationships among indoor second-hand smoking, household smoking rules, deprivation level and children mental health in a country-wide and population-based setting. Data was retrieved from and analysed in Scottish Health Survey, 2013. Information on demographics, indoor second-hand smoking status, household smoking rules, deprivation level and child mental health by Strengths and Difficulties Questionnaire was obtained by household interview through parents. Statistical analysis included chi-square test and survey-weighted logistic regression modelling. Of 1019 children aged 4-12, 17.9% (n = 182) lived in the 15% most deprivation areas. Deprived areas tended to be where indoor smoking occurred (p < 0.001). The top three sub-regions of the 15% most deprivation for Scottish children are greater Glasgow, Ayrshire & Arran and Forth Valley while the top three sub-regions of exposure to the indoor second-hand smoking are Fife, Forth Valley and Ayrshire & Arran. The top three sub-regions with indoor smoking allowed are greater Glasgow, Western Isles and Borders. Children emotional and behavioural problems were reduced when the strict household smoking rules (not allowed or outdoor areas) applied. One in six Scottish children lived in the 15% most deprivation areas and exposed to indoor second-hand smoking that could have led to emotional and behavioural problems. Public health programs promoting strict household smoking rules should be encouraged in order to optimise children mental health.

Identification of Cryptosporidium Species and Genotypes in Scottish Raw and Drinking Waters during a One-Year Monitoring Period▿

PubMed Central

Nichols, R. A. B.; Connelly, L.; Sullivan, C. B.; Smith, H. V.

2010-01-01

We analyzed 1,042 Cryptosporidium oocyst-positive slides (456 from raw waters and 586 from drinking waters) of which 55.7% contained 1 or 2 oocysts, to determine species/genotypes present in Scottish waters. Two nested PCR-restriction fragment length polymorphism (RFLP) assays targeting different loci (1 and 2) of the hypervariable region of the 18S rRNA gene were used for species identification, and 62.4% of samples were amplified with at least one of the PCR assays. More samples (577 slides; 48.7% from raw water and 51.3% from drinking water) were amplified at locus 1 than at locus 2 (419 slides; 50.1% from raw water and 49.9% from drinking water). PCR at loci 1 and 2 amplified 45.4% and 31.7% of samples containing 1 or 2 oocysts, respectively. We detected both human-infectious and non-human-infectious species/genotype oocysts in Scottish raw and drinking waters. Cryptosporidium andersoni, Cryptosporidium parvum, and the Cryptosporidium cervine genotype (now Cryptosporidium ubiquitum) were most commonly detected in both raw and drinking waters, with C. ubiquitum being most common in drinking waters (12.5%) followed by C. parvum (4.2%) and C. andersoni (4.0%). Numerous samples (16.6% total; 18.9% from drinking water) contained mixtures of two or more species/genotypes, and we describe strategies for unraveling their identity. Repetitive analysis for discriminating mixtures proved useful, but both template concentration and PCR assay influenced outcomes. Five novel Cryptosporidium spp. (SW1 to SW5) were identified by RFLP/sequencing, and Cryptosporidium sp. SW1 was the fourth most common contaminant of Scottish drinking water (3%). PMID:20639357

Ethnic variations in upper gastrointestinal hospitalizations and deaths: the Scottish Health and Ethnicity Linkage Study.

PubMed

Cezard, Genevieve I; Bhopal, Raj S; Ward, Hester J T; Bansal, Narinder; Bhala, Neeraj

2016-04-01

Upper gastrointestinal (GI) diseases are common, but there is a paucity of data describing variations by ethnic group and so a lack of understanding of potential health inequalities. We studied the incidence of specific upper GI hospitalization and death by ethnicity in Scotland. Using the Scottish Health and Ethnicity Linkage Study, linking NHS hospitalizations and mortality to the Scottish Census 2001, we explored ethnic differences in incidence (2001-10) of oesophagitis, peptic ulcer disease, gallstone disease and pancreatitis. Relative Risks (RRs) and 95% confidence intervals were calculated using Poisson regression, multiplied by 100, stratified by sex and adjusted for age, country of birth (COB) and socio-economic position. The White Scottish population (100) was the reference population. Ethnic variations varied by outcome and sex, e.g. adjusted RRs (95% confidence intervals) for oesophagitis were comparatively higher in Bangladeshi women (209; 124-352) and lower in Chinese men (65; 51-84) and women (69; 55-88). For peptic ulcer disease, RRs were higher in Chinese men (171; 131-223). Pakistani women had higher RRs for gallstone disease (129; 112-148) and pancreatitis (147; 109-199). The risks of upper GI diseases were lower in Other White British and Other White [e.g. for peptic ulcer disease in men, respectively (74; 64-85) and (81; 69-94)]. Risks of common upper GI diseases were comparatively lower in most White ethnic groups in Scotland. In non-White groups, however, risk varied by disease and ethnic group. These results require consideration in health policy, service planning and future research. © The Author 2015. Published by Oxford University Press on behalf of the European Public Health Association. All rights reserved.

Ethnicity and first birth: age, smoking, delivery, gestation, weight and feeding: Scottish Health and Ethnicity Linkage Study.

PubMed

Bansal, Narinder; Chalmers, James W T; Fischbacher, Colin M; Steiner, Markus F C; Bhopal, Raj S

2014-12-01

We linked census and health service data sets to address the shortage of information comparing maternal characteristics and pregnancy outcomes by ethnic group in Scotland. Retrospective cohort study linking the 2001 National Census for Scotland and hospital obstetric data (2001-08), comparing maternal age, smoking status, gestational age, caesarean section rates, birthweight, preterm birth and breastfeeding rates by ethnic group. In all, 144 344 women were identified as having had a first birth between 1 May 2001 and 30 April 2008. White Scottish mothers were younger [mean age 27.3 years; 95% confidence interval (CI): 27.3, 27.4] than other white groups and most non-white groups. They had the highest smoking rates (25.8%; CI: 25.5, 26.0) and the lowest rates of breastfeeding at 6-8 weeks (23.4%; CI: 23.1, 23.6), with most of the other groups being around 40%. Women from non-white minority ethnic groups in Scotland tended to have babies of lower birthweight (e.g. Pakistani mean birthweight-3105 g, white Scottish-3356 g), even after adjustment for gestational age, maternal age, education, smoking and housing tenure. This effect was more noticeable for women born in the UK. White English, Irish and other white babies tended to have higher birthweights. There was little variation between groups in caesarean section rates. Pregnant women from ethnic minority populations in Scotland have more favourable health behaviour than the white Scottish, although the non-white groups tend to have lower birthweight. Further exploration of the reasons for these differences has potential to benefit women from the majority population. © The Author 2014. Published by Oxford University Press on behalf of the European Public Health Association. All rights reserved.

Agreement between routine electronic hospital discharge and Scottish Stroke Care Audit (SSCA) data in identifying stroke in the Scottish population.

PubMed

Turner, Melanie; Barber, Mark; Dodds, Hazel; Dennis, Martin; Langhorne, Peter; Macleod, Mary-Joan

2015-12-30

In Scotland all non-obstetric, non-psychiatric acute inpatient and day case stays are recorded by an administrative hospital discharge database, the Scottish Morbidity Record (SMR01). The Scottish Stroke Care Audit (SSCA) collects data from all hospitals managing acute stroke in Scotland to support and improve quality of stroke care. The aim was to assess whether there were discrepancies between these data sources for admissions from 2010 to 2011. Records were matched when admission dates from the two data sources were within two days of each other and if an International Classification of Diseases (ICD) code of I61, I63, I64, or G45 was in the primary or secondary diagnosis field on SMR01. We also carried out a linkage analysis followed by a case-note review within one hospital in Scotland. There were a total of 22 416 entries on SSCA and 22 200 entries on SMR01. The concordance between SSCA and SMR01 was 16 823. SSCA contained 5593 strokes that were not present in SMR01, whereas SMR01 contained 185 strokes that were not present in SSCA. In the case-note review the concordance was 531, with SSCA containing 157 strokes that were not present in SMR01 and SMR01 containing 32 strokes that were not present in SSCA. When identifying strokes, hospital administrative discharge databases should be used with caution. Our results demonstrate that SSCA most accurately represents the number of strokes occurring in Scotland. This resource is useful for determining the provision of adequate patient care, stroke services and resources, and as a tool for research.

Anti-TNF therapy for paediatric IBD: the Scottish national experience.

PubMed

Cameron, F L; Wilson, M L; Basheer, N; Jamison, A; McGrogan, P; Bisset, W M; Gillett, P M; Russell, R K; Wilson, D C

2015-04-01

Biological agents are being increasingly used in the UK for paediatric-onset inflammatory bowel disease (PIBD) despite limited evidence and safety concerns. We evaluated effectiveness and safety in the clinical setting, highlighting drug cost pressures, using our national Scottish PIBD biological registry. Complete usage of the biological agents, infliximab (IFX) and adalimumab (ADA) for treatment of PIBD (in those aged <18 years) from 1 January 2000 to 30 September 2010 was collated from all treatments administered within the Scottish Paediatric Gastroenterology, Hepatology and Nutrition (PGHAN) national managed service network (all regional PGHAN centres and paediatric units within their associated district general hospitals). 132 children had biological therapy; 24 required both agents; 114 had Crohn's disease (CD), 16 had ulcerative colitis (UC) and 2 had IBD Unclassified (IBDU). 127 children received IFX to induce remission; 61 entered remission, 49 had partial response and 17 had no response. 72 were given maintenance IFX and 23 required dose escalation. 18 had infusion reactions and 27 had adverse events (infections/other adverse events). 29 had ADA to induce remission (28 CD and 1 UC), 24 after IFX; 10 entered remission, 12 had partial response and 7 had no response. All had maintenance; 19 required dose escalation. 12 children overall required hospitalisation due to drug toxicity. No deaths occurred with either IFX or ADA. Complete accrual of the Scottish nationwide 'real-life' experience demonstrates moderate effectiveness of anti tumour necrosis factor agents in severe PIBD but duration of effect is limited; significant financial issues (drug cost-need for dose escalation and/or multiple biological usage) and safety issues exist. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Prevalence of periradicular periodontitis in a Scottish subpopulation found on CBCT images.

PubMed

Dutta, A; Smith-Jack, F; Saunders, W P

2014-09-01

To investigate the prevalence of periradicular periodontitis (PRP) using cone-beam computed tomography (CBCT) scans in a retrospective cross-sectional epidemiological study in a Scottish subpopulation. Of the 319 CBCT scans performed at Dundee Dental Hospital between November 2009 and July 2012, 245 dentate scans of patients over 18 years of age were included and 3595 teeth examined. Odds ratios were calculated, and the association between root filling and posts with PRP was determined. Radiological signs of PRP were detected in 209 teeth (5.8%) in 96 patients (male = 53, female = 43) of which 145 (69.4%) were measurable and 64 (30.6%) appeared as periapical widening. Most lesions were seen in the 46-55-year age group and in maxillary anterior teeth (35.4%); 47.4% (n = 81) of the total root filled teeth (n = 171) had PRP. Of the root filled teeth with lesions, approximately half (50.6%) had an inadequate root filling. Teeth with crowns, but not root filled, accounted for 17.7% of PRP. Periapical changes were detected on a high proportion of teeth with post-retained crowns (70.7%). The presence of a root filling was significantly associated with PRP (z = 17.689 P < 0.0001; odds ratio 16.36 < 23.17 < 32.83, 95% CI) and the presence of a post (z = 10.901 P < 0.0001; odds ratio 21.36 < 41.8021 < 81.78, 95% CI). The prevalence of PRP in a Scottish subpopulation was 5.8%. The presence of a root filling or a post-retained crown was significantly associated with the presence of PRP as determined by CBCT scans. The prevalence of periradicular disease in root filled teeth remains high in the Scottish population. © 2013 International Endodontic Journal. Published by John Wiley & Sons Ltd.

Choosing the best method to estimate the energy density of a population using food purchase data.

PubMed

Wrieden, W L; Armstrong, J; Anderson, A S; Sherriff, A; Barton, K L

2015-04-01

Energy density (ED) is a measure of the energy content of a food component or diet relative to a standard unit of weight. Widespread variation in ED assessment methodologies exist. The present study aimed to explore the feasibility of calculating the ED of the Scottish diet using UK food purchase survey data and to identify the most appropriate method for calculating ED for use in the development of a Scottish Dietary Goal that captures any socioeconomic differences. Energy density was calculated using five different methods [food; food and milk; food, milk and energy containing (non-alcoholic) beverages; food, milk and all non-alcoholic beverages; and all food and beverages]. ED of the Scottish diet was estimated for each of the ED methods and data were examined by deprivation category. Mean ED varied from 409 to 847 kJ 100 g(-1) depending on the method used. ED values calculated from food (847 kJ 100 g(-1) ) and food and milk (718 kJ 100 g(-1) ) were most comparable to other published data, with the latter being a more accurate reflection of all food consumed. For these two methods, there was a significant gradient between the most and least deprived quintiles (892-807 and 737-696 kJ 100 g(-1) for food and food and milk, respectively). Because the World Cancer Research Fund recommendations are based on ED from food and milk, it was considered prudent to use this method for policy purposes and for future monitoring work of the Scottish Diet to ensure consistency of reporting and comparability with other published studies. © 2014 The British Dietetic Association Ltd.

Destination healthcare facility of shocked trauma patients in Scotland: analysis of transfusion and surgical capability of receiving hospitals.

PubMed

Peach, Christopher M; Morrison, Jonathan J; Apodaca, Amy N; Egan, Gerry; Watson, Henry G; Jansen, Jan O

2013-10-01

Haemorrhage is a leading cause of death from trauma. Management requires a combination of haemorrhage control and resuscitation which may incur significant surgical and transfusion utilisation. The aim of this study is to evaluate the resource provision of the destination hospital of Scottish trauma patients exhibiting evidence of pre-hospital shock. Patients who sustained a traumatic injury between November 2008 and October 2010 were retrospectively identified from the Scottish Ambulance Service electronic patients record system. Patients with a systolic blood pressure less than 110 mmHg or if missing, a heart rate greater than 120 bpm, were considered in shock. The level of the destination healthcare facility was classified in terms of surgical and transfusion capability. Patients with and without shock were compared. There were 135,004 patients identified, 133,651 (99.0%) of whom had sustained blunt trauma, 68,411 (50.7%) were male and the median (IQR) age was 59 (46). There were 6721 (5.0%) patients with shock, with a similar age and gender distribution to non-shocked patients. Only 1332 (19.8%) of shocked patients were taken to facilities with full surgical capability, 5137 (76.4%) to hospitals with limited (general and orthopaedic surgery only) and 252 (3.7%) to hospitals with no surgical services. In terms of transfusion capability, 5556 (82.7%) shocked patients were admitted to facilities with full capability and 1165 (17.3%) to a hospital with minimal or no capability. The majority of Scottish trauma patients are transported to a hospital with full transfusion capability, although the majority lack surgical sub-specialty representation. Copyright © 2013 Royal College of Surgeons of Edinburgh (Scottish charity number SC005317) and Royal College of Surgeons in Ireland. Published by Elsevier Ltd. All rights reserved.

The epidemiology of Scottish trauma: A comparison of pre-hospital and in-hospital deaths, 2000 to 2011.

PubMed

Morrison, Jonathan J; Yapp, Liam Z; Beattie, Anne; Devlin, Eimar; Samarage, Milan; McCaffer, Craig; Jansen, Jan O

2016-02-01

To characterise the temporal trends and urban-rural distribution of fatal injuries in Scotland through the analysis of mortality data collected by the National Records of Scotland. The prospectively collected NRS database was queried using ICD-10 codes for all Scottish trauma deaths during the period 2000 to 2011. Patients were divided into pre-hospital and in-hospital groups depending on the location of death. Incidence was plotted against time and linear regression was used to identify temporal trends. A total of 13,100 deaths were analysed. There were 4755 (36.3%) patients in the pre-hospital group with a median age (IQR) of 42 (28-58) years. The predominant cause of pre-hospital death related to vehicular injury (27.8%), which had a decreasing trend over the study period (p = 0.004). In-hospital, patients had a median age of 80 (58-88) years and the majority (67.0%) of deaths occurred following a fall on the level. This trend was shown to increase over the decade of study (p = 0.020). In addition, the incidence of urban incidents remained static, but the rate of rural fatal trauma decreased (p < 0.001). Around a third of Scottish trauma patients die prior to hospital admission and the predominant mechanism of injury is due to road traffic accidents. This contrasts with in-hospital deaths, which are mainly observed in elderly patients following a fall from standing height. Further research is required to determine the preventability of fatal traumatic injury in Scotland. Copyright © 2015 Royal College of Surgeons of Edinburgh (Scottish charity number SC005317) and Royal College of Surgeons in Ireland. Published by Elsevier Ltd. All rights reserved.

High-resolution ultrahigh-pressure long column reversed-phase liquid chromatography for top-down proteomics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shen, Yufeng; Tolic, Nikola; Piehowski, Paul D.

We report development of an approach providing high-resolution RPLC of proteins and its utility for mass spectrometry-based top-down proteomics. A chromatographic peak capacity of ~450 was achieved for proteins and large polypeptides having MWs up to 43 kDa in the context of proteomics applications. RPLC column lengths from 20 to 200 cm, particle sizes from 1.5 to 5 m, bonding alkyl chains from C1 to C2, C4, C8, and C18, and particle surface structures that spanned porous, superficially porous (porous shell, core-shell), and nonporous were investigated at pressures up to14K psi. Column length was found as the most important factormore » for >20 kDa proteins in gradient RPLC, and shortening column length degraded RPLC resolution and sensitivity regardless of the size and surface structure of the packing particles used. The alkyl chains bonded to the silica particle surface significantly affected the RPLC recovery and efficiency, and short alkyl C1-C4 phases provided higher sensitivity and resolution than C8 and C18 phases. Long gradient separations (e.g., >10 hours) with long columns (e.g., 100 cm) were particularly effective in conjunction with use of high accuracy mass spectrometers (e.g., the Orbitrap Elite) for top-down proteomics with improved proteoform coverage by allowing multiple HCD, CID, and ETD dissociation modes. It was also found that HCD produced small fragments useful for proteoform identification, while low energy CID and ETD often complemented HCD by providing large fragments.« less

Proteomic and phosphoproteomic analysis of polyethylene glycol-induced osmotic stress in root tips of common bean (Phaseolus vulgaris L.)

PubMed Central

Horst, Walter Johannes

2013-01-01

Previous studies have shown that polyethylene glycol (PEG)-induced osmotic stress (OS) reduces cell-wall (CW) porosity and limits aluminium (Al) uptake by root tips of common bean (Phaseolus vulgaris L.). A subsequent transcriptomic study suggested that genes related to CW processes are involved in adjustment to OS. In this study, a proteomic and phosphoproteomic approach was applied to identify OS-induced protein regulation to further improve our understanding of how OS affects Al accumulation. Analysis of total soluble proteins in root tips indicated that, in total, 22 proteins were differentially regulated by OS; these proteins were functionally categorized. Seventy-seven per- cent of the total expressed proteins were involved in metabolic pathways, particularly of carbohydrate and amino acid metabolism. An analysis of the apoplastic proteome revealed that OS reduced the level of five proteins and increased that of seven proteins. Investigation of the total soluble phosphoproteome suggested that dehydrin responded to OS with an enhanced phosphorylation state without a change in abundance. A cellular immunolocalization analysis indicated that dehydrin was localized mainly in the CW. This suggests that dehydrin may play a major protective role in the OS-induced physical breakdown of the CW structure and thus maintenance of the reversibility of CW extensibility during recovery from OS. The proteomic and phosphoproteomic analyses provided novel insights into the complex mechanisms of OS-induced reduction of Al accumulation in the root tips of common bean and highlight a key role for modification of CW structure. PMID:24123251

Automatic and rapid identification of glycopeptides by nano-UPLC-LTQ-FT-MS and proteomic search engine.

PubMed

Giménez, Estela; Gay, Marina; Vilaseca, Marta

2017-01-30

Here we demonstrate the potential of nano-UPLC-LTQ-FT-MS and the Byonic™ proteomic search engine for the separation, detection, and identification of N- and O-glycopeptide glycoforms in standard glycoproteins. The use of a BEH C18 nanoACQUITY column allowed the separation of the glycopeptides present in the glycoprotein digest and a baseline-resolution of the glycoforms of the same glycopeptide on the basis of the number of sialic acids. Moreover, we evaluated several acquisition strategies in order to improve the detection and characterization of glycopeptide glycoforms with the maximum number of identification percentages. The proposed strategy is simple to set up with the technology platforms commonly used in proteomic labs. The method allows the straightforward and rapid obtention of a general glycosylated map of a given protein, including glycosites and their corresponding glycosylated structures. The MS strategy selected in this work, based on a gas phase fractionation approach, led to 136 unique peptides from four standard proteins, which represented 78% of the total number of peptides identified. Moreover, the method does not require an extra glycopeptide enrichment step, thus preventing the bias that this step could cause towards certain glycopeptide species. Data are available via ProteomeXchange with identifier PXD003578. We propose a simple and high-throughput glycoproteomics-based methodology that allows the separation of glycopeptide glycoforms on the basis of the number of sialic acids, and their automatic and rapid identification without prior knowledge of protein glycosites or type and structure of the glycans. Copyright © 2016 Elsevier B.V. All rights reserved.

Improving the quality and impact of public health social media activity in Scotland during 2016: #ScotPublicHealth.

PubMed

Mackenzie, Douglas Graham

2017-06-07

Social media, including Twitter, potentially provides a route to communicate public health messages to a large audience. Simple measures can boost onward broadcast to other users ('retweeting'). This study compares the impact of a structured programme of social media activity in Scotland during 2016 (using #ScotPublicHealth hashtag) with previous years. The Twitter search function was used to identify tweets between 2014 and 2016 inclusive. The first three tweets from each Twitter user were selected for each period. The number of retweets was used as a measure of impact. The quality of tweets was assessed by recording use of image, weblink (uniform resource locator or URL), mention of another Twitter user and/or hashtag, each of which have been shown to boost number of retweets. The percentage of tweets with an image, URL and/or mention of another Twitter user increased during the period of study. The percentage of tweets retweeted during Scottish Public Health conferences increased from 43% in 2014 to 70% in 2016. The volume of tweeting also increased. The quality and impact of tweets sent by the Scottish Public Health community was higher during 2016 than previous years. Conference tweeting remains an area for improvement. © The Author 2017. Published by Oxford University Press on behalf of Faculty of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Supporting staff in employment: the emotional wellbeing of staff in an NHS psychiatric hospital.

PubMed

Patterson, I D; Bell, J S

2000-09-01

The objective of this study was to assess the emotional wellbeing of a broad sample of NHS employees in a psychiatric setting; to seek their views on sources of distress; and to identify preferred ways of dealing with it. A cross-sectional postal survey, employing two questionnaires: GHQ-28, and a semi-structured questionnaire. These were sent to a nominal 50% sample (n = 599). The population was the staff of a large Scottish psychiatric service. A 47.9% response rate was achieved; 32.9% of respondents exceeded a cut-off score of four on the GHQ-28. Neither occupational, group nor gender effects were significant on this measure. The reporting of emotionally-distressing problems affecting their performance was found to be more common amongst doctors; males, overall, showed a non-significant trend towards having been affected more than females by such problems; and older staff (above 45) were affected significantly more often than younger staff. Almost a third of staff were unaware of the availability of an internal organisational resource (the Occupational Health service). NHS Trusts should ensure the culture at work is appropriate from a preventative point of view and be aware that factors outwith the workplace can affect employees emotional wellbeing and performance. Preventative and supportive measures to minimise psychological distress in the workforce should be considered; the Scottish Needs Assessment Programme: Mental Health in the Workplace offers useful guidance.

Barriers to accessing termination of pregnancy in a remote and rural setting: a qualitative study.

PubMed

Heller, R; Purcell, C; Mackay, L; Caird, L; Cameron, S T

2016-09-01

To explore the experiences of women from a remote and rural setting who had a termination of pregnancy (TOP), in relation to any barriers they may have experienced trying to access TOP. Qualitative interview study. Scottish Highlands and Western Isles. Women who had undergone TOP in the Scottish Highlands National Health Service between October 2014 and May 2015. Sixteen semi-structured, audio-recorded telephone interviews were conducted by a researcher with women who had consented to be interviewed at their initial assessment. Six stages of thematic analysis were followed to explore themes in and across participant accounts. Themes derived from interview transcripts. Four themes emerged relating to barriers to access and experience: (1) the impact of travel for TOP, (2) temporal factors unique to this population and how they affected women, (3) the attitude of health professionals, notably general practitioners, as a result of local culture, and (4) stigma surrounding TOP and the expectation that abortion will be traumatising. Women in remote and rural areas experience barriers to accessing TOP. Prompt referrals, more providers of TOP and tackling stigma associated with TOP could make delivery of this service more equitable and improve women's journey through TOP. Women in remote and rural areas of Scotland face multiple barriers to accessing termination of pregnancy. © 2016 Royal College of Obstetricians and Gynaecologists.

A Proteome-wide Domain-centric Perspective on Protein Phosphorylation *

PubMed Central

Palmeri, Antonio; Ausiello, Gabriele; Ferrè, Fabrizio; Helmer-Citterich, Manuela; Gherardini, Pier Federico

2014-01-01

Phosphorylation is a widespread post-translational modification that modulates the function of a large number of proteins. Here we show that a significant proportion of all the domains in the human proteome is significantly enriched or depleted in phosphorylation events. A substantial improvement in phosphosites prediction is achieved by leveraging this observation, which has not been tapped by existing methods. Phosphorylation sites are often not shared between multiple occurrences of the same domain in the proteome, even when the phosphoacceptor residue is conserved. This is partly because of different functional constraints acting on the same domain in different protein contexts. Moreover, by augmenting domain alignments with structural information, we were able to provide direct evidence that phosphosites in protein-protein interfaces need not be positionally conserved, likely because they can modulate interactions simply by sitting in the same general surface area. PMID:24830415

Comprehensive and Quantitative Proteomic Analysis of Metamorphosis-Related Proteins in the Veined Rapa Whelk, Rapana venosa.

PubMed

Song, Hao; Wang, Hai-Yan; Zhang, Tao

2016-06-15

Larval metamorphosis of the veined rapa whelk (Rapana venosa) is a pelagic to benthic transition that involves considerable structural and physiological changes. Because metamorphosis plays a pivotal role in R. venosa commercial breeding and natural populations, the endogenous proteins that drive this transition attract considerable interest. This study is the first to perform a comprehensive and quantitative proteomic analysis related to metamorphosis in a marine gastropod. We analyzed the proteomes of competent R. venosa larvae and post-larvae, resulting in the identification of 5312 proteins, including 470 that were downregulated and 668 that were upregulated after metamorphosis. The differentially expressed proteins reflected multiple processes involved in metamorphosis, including cytoskeleton and cell adhesion, ingestion and digestion, stress response and immunity, as well as specific tissue development. Our data improve understanding of the physiological traits controlling R. venosa metamorphosis and provide a solid basis for further study.

Systematically Ranking the Tightness of Membrane Association for Peripheral Membrane Proteins (PMPs)*

PubMed Central

Gao, Liyan; Ge, Haitao; Huang, Xiahe; Liu, Kehui; Zhang, Yuanya; Xu, Wu; Wang, Yingchun

2015-01-01

Large-scale quantitative evaluation of the tightness of membrane association for nontransmembrane proteins is important for identifying true peripheral membrane proteins with functional significance. Herein, we simultaneously ranked more than 1000 proteins of the photosynthetic model organism Synechocystis sp. PCC 6803 for their relative tightness of membrane association using a proteomic approach. Using multiple precisely ranked and experimentally verified peripheral subunits of photosynthetic protein complexes as the landmarks, we found that proteins involved in two-component signal transduction systems and transporters are overall tightly associated with the membranes, whereas the associations of ribosomal proteins are much weaker. Moreover, we found that hypothetical proteins containing the same domains generally have similar tightness. This work provided a global view of the structural organization of the membrane proteome with respect to divergent functions, and built the foundation for future investigation of the dynamic membrane proteome reorganization in response to different environmental or internal stimuli. PMID:25505158

'Gate effect' in templated polyacrylamide membranes influences the electrotransport of proteins and finds applications in proteome analysis.

PubMed

Bossi, Alessandra; Andreoli, Matteo; Bonini, Francesca; Piletsky, Sergey

2007-09-01

Templating is an effective way for the structural modifications of a material and hence for altering its functional properties. Here protein imprinting was exploited to alter polymeric polyacrylamide (PAA) membranes. The sieving properties and selection abilities of the material formed were evaluated by studying the electrically driven transport of various proteins across templated PAA membranes. The sieving properties correlated with the templating process and depended on the quantity of template used during the polymerisation. For 1 mg/mL protein-templated membranes a 'gate effect' was shown, which induced a preferential migration of the template and of similar-size proteins. Such template preferential electrotransport was exploited for the selective removal of certain proteins in biological fluids prior to proteome analysis (depletion of albumin from human serum); the efficiency of the removal was demonstrated by analysing the serum proteome by two-dimensional electrophoresis experiments.

Optimizing of MALDI-ToF-based low-molecular-weight serum proteome pattern analysis in detection of breast cancer patients; the effect of albumin removal on classification performance.

PubMed

Pietrowska, M; Marczak, L; Polanska, J; Nowicka, E; Behrent, K; Tarnawski, R; Stobiecki, M; Polanski, A; Widlak, P

2010-01-01

Mass spectrometry-based analysis of the serum proteome allows identifying multi-peptide patterns/signatures specific for blood of cancer patients, thus having high potential value for cancer diagnostics. However, because of problems with optimization and standardization of experimental and computational design, none of identified proteome patterns/signatures was approved for diagnostics in clinical practice as yet. Here we compared two methods of serum sample preparation for mass spectrometry-based proteome pattern analysis aimed to identify biomarkers that could be used in early detection of breast cancer patients. Blood samples were collected in a group of 92 patients diagnosed at early (I and II) stages of the disease before the start of therapy, and in a group of age-matched healthy controls (104 women). Serum specimens were purified and analyzed using MALDI-ToF spectrometry, either directly or after membrane filtration (50 kDa cut-off) to remove albumin and other large serum proteins. Mass spectra of the low-molecular-weight fraction (2-10 kDa) of the serum proteome were resolved using the Gaussian mixture decomposition, and identified spectral components were used to build classifiers that differentiated samples from breast cancer patients and healthy persons. Mass spectra of complete serum and membrane-filtered albumin-depleted samples have apparently different structure and peaks specific for both types of samples could be identified. The optimal classifier built for the complete serum specimens consisted of 8 spectral components, and had 81% specificity and 72% sensitivity, while that built for the membrane-filtered samples consisted of 4 components, and had 80% specificity and 81% sensitivity. We concluded that pre-processing of samples to remove albumin might be recommended before MALDI-ToF mass spectrometric analysis of the low-molecular-weight components of human serum Keywords: albumin removal; breast cancer; clinical proteomics; mass spectrometry; pattern analysis; serum proteome.

Spermatogenesis in mammals: proteomic insights.

PubMed

Chocu, Sophie; Calvel, Pierre; Rolland, Antoine D; Pineau, Charles

2012-08-01

Spermatogenesis is a highly sophisticated process involved in the transmission of genetic heritage. It includes halving ploidy, repackaging of the chromatin for transport, and the equipment of developing spermatids and eventually spermatozoa with the advanced apparatus (e.g., tightly packed mitochondrial sheat in the mid piece, elongating of the tail, reduction of cytoplasmic volume) to elicit motility once they reach the epididymis. Mammalian spermatogenesis is divided into three phases. In the first the primitive germ cells or spermatogonia undergo a series of mitotic divisions. In the second the spermatocytes undergo two consecutive divisions in meiosis to produce haploid spermatids. In the third the spermatids differentiate into spermatozoa in a process called spermiogenesis. Paracrine, autocrine, juxtacrine, and endocrine pathways all contribute to the regulation of the process. The array of structural elements and chemical factors modulating somatic and germ cell activity is such that the network linking the various cellular activities during spermatogenesis is unimaginably complex. Over the past two decades, advances in genomics have greatly improved our knowledge of spermatogenesis, by identifying numerous genes essential for the development of functional male gametes. Large-scale analyses of testicular function have deepened our insight into normal and pathological spermatogenesis. Progress in genome sequencing and microarray technology have been exploited for genome-wide expression studies, leading to the identification of hundreds of genes differentially expressed within the testis. However, although proteomics has now come of age, the proteomics-based investigation of spermatogenesis remains in its infancy. Here, we review the state-of-the-art of large-scale proteomic analyses of spermatogenesis, from germ cell development during sex determination to spermatogenesis in the adult. Indeed, a few laboratories have undertaken differential protein profiling expression studies and/or systematic analyses of testicular proteomes in entire organs or isolated cells from various species. We consider the pros and cons of proteomics for studying the testicular germ cell gene expression program. Finally, we address the use of protein datasets, through integrative genomics (i.e., combining genomics, transcriptomics, and proteomics), bioinformatics, and modelling.

Comparative proteomics of matrix fractions between pimpled and normal chicken eggshells.

PubMed

Liu, Zhangguo; Song, Lingzi; Lu, Lizhi; Zhang, Xianfu; Zhang, Fuming; Wang, Kehua; Linhardt, Robert J

2017-09-07

Eggshell matrix can be dissociated into three matrix fractions: acid-insoluble matrix (M1), water-insoluble matrix (M2) and acid-water facultative-soluble matrix (M3). Matrix fractions from pimpled and normal eggshells were compared using label-free proteomic method to understand the differences among three matrix fractions and the proteins involved with eggshell quality. A total of 738 and 600 proteins were identified in the pimpled and normal calcified eggshells, respectively. Both eggshells showed a combined proteomic inventory of 769 proteins. In the same type of eggshell, a high similarity was present in the proteomes of three matrix fractions. These triply overlapped common proteins formed the predominant contributor to proteomic abundance in the matrix fractions. In each matrix fraction and between both eggshell models, normal and pimpled eggshells, a majority of the proteomes of the fractions were commonly observed. Forty-two common major proteins (iBAQ-derived abundance ≥0.095% of proteomic abundance) were identified throughout the three matrix fractions and these proteins might act as backbone constituents in chicken eggshell matrix. Finally, using 1.75-fold as up-regulated and using 0.57-fold as down-regulated cutoff values, twenty-five differential major proteins were screened and they all negatively influence and none showed any effect on eggshell quality. Overall, we uncovered the characteristics of proteomics of three eggshell matrix fractions and identified candidate proteins influencing eggshell quality. The next research on differential proteins will uncover the potential mechanisms underlying how proteins affect eggshell quality. It was reported that the proteins in an eggshell can be divided into insoluble and soluble proteins. The insoluble proteins are thought to be an inter-mineral matrix and acts as a structural framework, while the soluble proteins are thought as intra-mineral matrix that are embedded within the crystal during calcification. However, the difference between matrix fractions is unknown. Cross-analysis of proteomic data of three matrix fractions from the same type of eggshell, uncovered triply overlapped common proteins formed the predominant contributor to proteomic abundance of any matrix fraction, and we suggested that abundance variance of some common proteins between the three matrix fractions might be an important cause of their solubility differences. Moreover, eggshell is formed in hen's uterus, and uterus tend to be considered as unique organ determining eggshell quality. By cross-analysis on proteomic data of three matrix fractions between two eggshell models, normal and pimpled eggshells, the differential proteins were screened as candidates influencing eggshell quality. And we suggested that the liver and spleen or lymphocytes might be the major organs influencing eggshell quality, because the most promising candidates are almost blood and non-collagenous proteins, and originated from above organs. Copyright © 2017 Elsevier B.V. All rights reserved.

Bank stability as a risk factor for pipeline infrastructure: a Scottish example

NASA Astrophysics Data System (ADS)

Maniatis, Georgios; Williams, Richard; Hoey, Trevor

2017-04-01

Bank erosion is a spatially variable process controlled by a number of factors that are interrelated (e.g. grain size, moisture content, organic content, vegetation, bank gradient). As a risk factor, bank erosion has been strongly connected to the failure of infrastructure that crosses or is adjacent to morphologically dynamic rivers. To manage this risk, comprehensive infrastructure asset management programs should include risk assessment of all structures that cross or are near a river. In Scotland, a significant proportion of cross-river infrastructure is pipe bridges, for both clean and waste water. These river crossings are maintained and managed by Scottish Water, a supplier responsible for a 48,000 km long drinking water pipe network and a 52,000 km long wastewater pipe network. Recently, Scottish Water began a comprehensive pipe bridge asset inspection program, which incorporates the acquisition of data to assess riverbank stability. The first step in the development of this database is the use of a prototype software application (a tablet app) which simplifies the surveying process by framing specific geomorphological questions and surveying tasks. As a result, the surveys can be conducted by inspectors with no specialist training in bank stability assessment and then reviewed by those with more expertise. Here, results are presented of a review of survey data, enabling the identification of the assets that are most at risk from bank erosion. The assessment focuses on assets from catchments in two contrasting areas of Scotland; the Hebrides and Glasgow. The uncertainty analysis focuses on input data quality and the variability of information available for desk based risk assessments using Geographic Information Systems (GIS). In parallel, considerations regarding the extension of this framework towards a unified strategy for assessing bank erosion are discussed such as the selection of a statistical framework and the catchment classification process. Finally, we discuss the process of knowledge exchange, where an industrial organization benefits from the scientific input and the academic organization benefits from the access to rapid surveying input at a country scale.

Proteomic and metabolomic analysis on the toxicological effects of As (III) and As (V) in juvenile mussel Mytilus galloprovincialis.

PubMed

Yu, Deliang; Ji, Chenglong; Zhao, Jianmin; Wu, Huifeng

2016-05-01

Inorganic arsenic (As) is a known pollutant including two chemical forms (arsenite (As III) and arsenate (As V)), in marine and coastal environment. Marine mussel Mytilus galloprovincialis is an important environmental monitoring species around the world. In this study, we focused on valence-specific responses of As in juvenile mussel M. galloprovincialis using a combined proteomic and metabolomic approach. Metabolic responses indicated that As (III) mainly caused disturbance in osmotic regulation in juvenile mussels. As (V) caused disturbances in both osmotic regulation and energy metabolism marked by different metabolic responses, including betaine, taurine, glucose and glycogen. Proteomic responses exhibited that As (III) had a significant negative effect on cytoskeleton and cell structure (actin and collagen alpha-6(VI) chain). As (V) affected some key enzymes involved in energy metabolism (cytosolic malate dehydrogenase, cMDH) and cell development (ornithine aminotransferase and astacin). Overall, all these results confirmed the valence-specific responses in juvenile mussels to As exposures. These findings demonstrate that a combined metabolomic and proteomic approach could provide an important insight into the toxicological effects of environmental pollutants in organisms. Copyright © 2016 Elsevier Ltd. All rights reserved.

Proteomics Analysis of the Nucleolus in Adenovirus-infected Cells

PubMed Central

Lam, Yun W.; Evans, Vanessa C.; Heesom, Kate J.; Lamond, Angus I.; Matthews, David A.

2010-01-01

Adenoviruses replicate primarily in the host cell nucleus, and it is well established that adenovirus infection affects the structure and function of host cell nucleoli in addition to coding for a number of nucleolar targeted viral proteins. Here we used unbiased proteomics methods, including high throughput mass spectrometry coupled with stable isotope labeling by amino acids in cell culture (SILAC) and traditional two-dimensional gel electrophoresis, to identify quantitative changes in the protein composition of the nucleolus during adenovirus infection. Two-dimensional gel analysis revealed changes in six proteins. By contrast, SILAC-based approaches identified 351 proteins with 24 proteins showing at least a 2-fold change after infection. Of those, four were previously reported to have aberrant localization and/or functional relevance during adenovirus infection. In total, 15 proteins identified as changing in amount by proteomics methods were examined in infected cells using confocal microscopy. Eleven of these proteins showed altered patterns of localization in adenovirus-infected cells. Comparing our data with the effects of actinomycin D on the nucleolar proteome revealed that adenovirus infection apparently specifically targets a relatively small subset of nucleolar antigens at the time point examined. PMID:19812395

Proteomics analysis of the nucleolus in adenovirus-infected cells.

PubMed

Lam, Yun W; Evans, Vanessa C; Heesom, Kate J; Lamond, Angus I; Matthews, David A

2010-01-01

Adenoviruses replicate primarily in the host cell nucleus, and it is well established that adenovirus infection affects the structure and function of host cell nucleoli in addition to coding for a number of nucleolar targeted viral proteins. Here we used unbiased proteomics methods, including high throughput mass spectrometry coupled with stable isotope labeling by amino acids in cell culture (SILAC) and traditional two-dimensional gel electrophoresis, to identify quantitative changes in the protein composition of the nucleolus during adenovirus infection. Two-dimensional gel analysis revealed changes in six proteins. By contrast, SILAC-based approaches identified 351 proteins with 24 proteins showing at least a 2-fold change after infection. Of those, four were previously reported to have aberrant localization and/or functional relevance during adenovirus infection. In total, 15 proteins identified as changing in amount by proteomics methods were examined in infected cells using confocal microscopy. Eleven of these proteins showed altered patterns of localization in adenovirus-infected cells. Comparing our data with the effects of actinomycin D on the nucleolar proteome revealed that adenovirus infection apparently specifically targets a relatively small subset of nucleolar antigens at the time point examined.

Proteomic Investigations into Hemodialysis Therapy

PubMed Central

Bonomini, Mario; Sirolli, Vittorio; Pieroni, Luisa; Felaco, Paolo; Amoroso, Luigi; Urbani, Andrea

2015-01-01

The retention of a number of solutes that may cause adverse biochemical/biological effects, called uremic toxins, characterizes uremic syndrome. Uremia therapy is based on renal replacement therapy, hemodialysis being the most commonly used modality. The membrane contained in the hemodialyzer represents the ultimate determinant of the success and quality of hemodialysis therapy. Membrane’s performance can be evaluated in terms of removal efficiency for unwanted solutes and excess fluid, and minimization of negative interactions between the membrane material and blood components that define the membrane’s bio(in)compatibility. Given the high concentration of plasma proteins and the complexity of structural functional relationships of this class of molecules, the performance of a membrane is highly influenced by its interaction with the plasma protein repertoire. Proteomic investigations have been increasingly applied to describe the protein uremic milieu, to compare the blood purification efficiency of different dialyzer membranes or different extracorporeal techniques, and to evaluate the adsorption of plasma proteins onto hemodialysis membranes. In this article, we aim to highlight investigations in the hemodialysis setting making use of recent developments in proteomic technologies. Examples are presented of why proteomics may be helpful to nephrology and may possibly affect future directions in renal research. PMID:26690416

MAPA distinguishes genotype-specific variability of highly similar regulatory protein isoforms in potato tuber.

PubMed

Hoehenwarter, Wolfgang; Larhlimi, Abdelhalim; Hummel, Jan; Egelhofer, Volker; Selbig, Joachim; van Dongen, Joost T; Wienkoop, Stefanie; Weckwerth, Wolfram

2011-07-01

Mass Accuracy Precursor Alignment is a fast and flexible method for comparative proteome analysis that allows the comparison of unprecedented numbers of shotgun proteomics analyses on a personal computer in a matter of hours. We compared 183 LC-MS analyses and more than 2 million MS/MS spectra and could define and separate the proteomic phenotypes of field grown tubers of 12 tetraploid cultivars of the crop plant Solanum tuberosum. Protein isoforms of patatin as well as other major gene families such as lipoxygenase and cysteine protease inhibitor that regulate tuber development were found to be the primary source of variability between the cultivars. This suggests that differentially expressed protein isoforms modulate genotype specific tuber development and the plant phenotype. We properly assigned the measured abundance of tryptic peptides to different protein isoforms that share extensive stretches of primary structure and thus inferred their abundance. Peptides unique to different protein isoforms were used to classify the remaining peptides assigned to the entire subset of isoforms based on a common abundance profile using multivariate statistical procedures. We identified nearly 4000 proteins which we used for quantitative functional annotation making this the most extensive study of the tuber proteome to date.

Proteomic profiling of the human T-cell nucleolus.

PubMed

Jarboui, Mohamed Ali; Wynne, Kieran; Elia, Giuliano; Hall, William W; Gautier, Virginie W

2011-12-01

The nucleolus, site of ribosome biogenesis, is a dynamic subnuclear organelle involved in diverse cellular functions. The size, number and organisation of nucleoli are cell-specific and while it remains to be established, the nucleolar protein composition would be expected to reflect lineage-specific transcriptional regulation of rDNA genes and have cell-type functional components. Here, we describe the first characterisation of the human T-cell nucleolar proteome. Using the Jurkat T-cell line and a reproducible organellar proteomic approach, we identified 872 nucleolar proteins. In addition to ribosome biogenesis and RNA processing networks, network modeling and topological analysis of nucleolar proteome revealed distinct macromolecular complexes known to orchestrate chromatin structure and to contribute to the regulation of gene expression, replication, recombination and repair, and chromosome segregation. Furthermore, among our dataset, we identified proteins known to functionally participate in T-cell biology, including RUNX1, ILF3, ILF2, STAT3, LSH, TCF-1, SATB1, CTCF, HMGB3, BCLAF1, FX4L1, ZAP70, TIAM1, RAC2, THEMIS, LCP1, RPL22, TOPK, RETN, IFI-16, MCT-1, ISG15, and 14-3-3τ, which support cell-specific composition of the Jurkat nucleolus. Subsequently, the nucleolar localisation of RUNX1, ILF3, STAT3, ZAP70 and RAC2 was further validated by Western Blot analysis and immunofluorescence microscopy. Overall, our T-cell nucleolar proteome dataset not only further expands the existing repertoire of the human nucleolar proteome but support a cell type-specific composition of the nucleolus in T cell and highlights the potential roles of the nucleoli in lymphocyte biology. Copyright © 2011 Elsevier Ltd. All rights reserved.

The nuclear proteome of Trypanosoma brucei

PubMed Central

Goos, Carina; Dejung, Mario; Janzen, Christian J.; Butter, Falk

2017-01-01

Trypanosoma brucei is a protozoan flagellate that is transmitted by tsetse flies into the mammalian bloodstream. The parasite has a huge impact on human health both directly by causing African sleeping sickness and indirectly, by infecting domestic cattle. The biology of trypanosomes involves some highly unusual, nuclear-localised processes. These include polycistronic transcription without classical promoters initiated from regions defined by histone variants, trans-splicing of all transcripts to the exon of a spliced leader RNA, transcription of some very abundant proteins by RNA polymerase I and antigenic variation, a switch in expression of the cell surface protein variants that allows the parasite to resist the immune system of its mammalian host. Here, we provide the nuclear proteome of procyclic Trypanosoma brucei, the stage that resides within the tsetse fly midgut. We have performed quantitative label-free mass spectrometry to score 764 significantly nuclear enriched proteins in comparison to whole cell lysates. A comparison with proteomes of several experimentally characterised nuclear and non-nuclear structures and pathways confirmed the high quality of the dataset: the proteome contains about 80% of all nuclear proteins and less than 2% false positives. Using motif enrichment, we found the amino acid sequence KRxR present in a large number of nuclear proteins. KRxR is a sub-motif of a classical eukaryotic monopartite nuclear localisation signal and could be responsible for nuclear localization of proteins in Kinetoplastida species. As a proof of principle, we have confirmed the nuclear localisation of six proteins with previously unknown localisation by expressing eYFP fusion proteins. While proteome data of several T. brucei organelles have been published, our nuclear proteome closes an important gap in knowledge to study trypanosome biology, in particular nuclear-related processes. PMID:28727848

News Conference: The Big Bangor Day Meeting Lecture: Charterhouse plays host to a physics day Festival: Science on Stage festival 2013 arrives in Poland Event: Scottish Physics Teachers' Summer School Meeting: Researchers and educators meet at Lund University Conference: Exeter marks the spot Recognition: European Physical Society uncovers an historic site Education: Initial teacher education undergoes big changes Forthcoming events

NASA Astrophysics Data System (ADS)

2013-09-01

Conference: The Big Bangor Day Meeting Lecture: Charterhouse plays host to a physics day Festival: Science on Stage festival 2013 arrives in Poland Event: Scottish Physics Teachers' Summer School Meeting: Researchers and educators meet at Lund University Conference: Exeter marks the spot Recognition: European Physical Society uncovers an historic site Education: Initial teacher education undergoes big changes Forthcoming events

Intimacy and the life cycle in the marital relationships of the Scottish elite during the long eighteenth century.

PubMed

Barclay, Katie

2011-01-01

Traditionally marriage has been treated as one step in the life cycle, between youth and old age, singleness and widowhood. Yet an approach to the life cycle that treats marriage as a single step in a person's life is overly simplistic. During the eighteenth century many marriages were of considerable longevity during which time couples aged together and power dynamics within the home were frequently renegotiated to reflect changing circumstances. This study explores how intimacy developed and changed over the life cycle of marriage and what this meant for power, through a study of the correspondence of two elite Scottish couples.

Deprivation and self-reported health: are there 'Scottish effects' in England and Wales?

PubMed

Whynes, David K

2009-03-01

Although the association between poor health and deprivation is well-founded, a 'Scottish effect' has been observed, whereby the level of health appears even poorer than Scotland's higher level of deprivation should warrant. We consider whether 'Scottish effects' also occur within the regions of England and Wales. Using ward-level data from the national census, we regress healthy life expectancies relative to total life expectancies on Carstairs deprivation scores, households' average disposable incomes, geo-spatial characteristics and regional dummy variables. Higher incomes and lower Carstairs scores are each associated with longer proportions of lives expected to be spent in good health or without long-standing illness. Relative to the London region, the coefficients on the regional dummies are uniformly negative and mostly significant. There exist differences in relative health expectancies between the regions of England and Wales, which are not fully explained by the differences in socio-economic circumstances. Conventional deprivation measures tend to understate the poorer health performances of the more deprived regions (Wales and the north of England), and the understatement increases with deprivation. The exception to the rule is London, where health expectancies are superior to those which deprivation leads us to expect.

Genetic epidemiology of motor neuron disease-associated variants in the Scottish population.

PubMed

Black, Holly A; Leighton, Danielle J; Cleary, Elaine M; Rose, Elaine; Stephenson, Laura; Colville, Shuna; Ross, David; Warner, Jon; Porteous, Mary; Gorrie, George H; Swingler, Robert; Goldstein, David; Harms, Matthew B; Connick, Peter; Pal, Suvankar; Aitman, Timothy J; Chandran, Siddharthan

2017-03-01

Genetic understanding of motor neuron disease (MND) has evolved greatly in the past 10 years, including the recent identification of association between MND and variants in TBK1 and NEK1. Our aim was to determine the frequency of pathogenic variants in known MND genes and to assess whether variants in TBK1 and NEK1 contribute to the burden of MND in the Scottish population. SOD1, TARDBP, OPTN, TBK1, and NEK1 were sequenced in 441 cases and 400 controls. In addition to 44 cases known to carry a C9orf72 hexanucleotide repeat expansion, we identified 31 cases and 2 controls that carried a loss-of-function or pathogenic variant. Loss-of-function variants were found in TBK1 in 3 cases and no controls and, separately, in NEK1 in 3 cases and no controls. This study provides an accurate description of the genetic epidemiology of MND in Scotland and provides support for the contribution of both TBK1 and NEK1 to MND susceptibility in the Scottish population. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Edinburgh, the Scottish pioneers of anatomy and their lasting influence in South Africa.

PubMed

Correia, J C; Wessels, Q; Vorster, W

2013-11-01

The history of the origin of anatomy education in South Africa is the history of an arduous journey through time. The lasting influence of Edinburgh came in the form of Robert Black Thomson. He was a student and assistant of Sir William Turner who gave rise to the first chair of anatomy and the establishment of a department at the South African College, known today as University of Cape Town. Thomson was later succeeded by Matthew Drennan, a keen anthropologist, who was revered by his students. This Scottish link prevailed over time with the appointment of Edward Philip Stibbe as the chair of anatomy at the South African School of Mines and Technology, which later became the University of the Witwatersrand. Stibbe's successor, Raymond Arthur Dart, a graduate of the University of Sydney, was trained in an anatomy department sculpted on that of Edinburgh by Professor James Thomas Wilson. Wilson's influence at the University of Sydney can be traced back to Edinburgh and William Turner through Thomas Anderson Stuart. Both Dart and Robert Broom, another Scot, were considered as Africa's wild men by the late Professor Tobias. Here, the authors explore the Scottish link and origins of anatomy pedagogy in South Africa.

The value of chest X-ray in the Scottish Referral Guidelines for suspected head and neck cancer in 2144 patients.

PubMed

Fingland, P; Carswell, V; Tikka, T; Douglas, C M; Montgomery, J

2018-04-30

In Scotland, patients with suspected head and neck cancer are referred on the basis of the Scottish Referral Guidelines for Suspected Cancer, rather than the National Institute for Health and Care Excellence guidelines. A chest X-ray should be requested by the general practitioner at the same time as referral for persistent hoarseness. The evidence for this is level 4. This audit identified adherence to this recommendation and X-ray results. All 'urgent suspicion of cancer' referrals to the ENT department in the National Health Service Greater Glasgow and Clyde for 2015-2016 were audited. Persistent hoarseness for more than 3 weeks instigated referral in 318 patients (15.7 per cent). Chest X-ray was performed in 120 patients (38 per cent), which showed: no abnormality in 116 (96.7 per cent), features of infection in 2 (1.7 per cent) and something else in 2 patients (1.7 per cent). No chest X-ray altered the management of a patient. Performance of chest X-ray does not alter management and its removal from the Scottish Referral Guidelines for Suspected Cancer is recommended.

Family size and perinatal circumstances, as mental health risk factors in a Scottish birth cohort.

PubMed

Riordan, Daniel Vincent; Morris, Carole; Hattie, Joanne; Stark, Cameron

2012-06-01

Higher maternal parity and younger maternal age have each been observed to be associated with subsequent offspring suicidal behaviour. This study aimed to establish if these, and other variables from the perinatal period, together with family size, are also associated with other psychiatric morbidity. Linked datasets of the Scottish Morbidity Record and Scottish death records were used to follow up, into young adulthood, a birth cohort of 897,685. In addition to the index maternity records, mothers' subsequent pregnancy records were identified, allowing family size to be estimated. Three independent outcomes were studied: suicide, self-harm, and psychiatric hospital admission. Data were analysed using Cox regression. Younger maternal age and higher maternal parity were independently associated with increased risk in offspring of suicide, of self-harm and of psychiatric admission. Risk of psychiatric admission was higher amongst those from families of three or more, but, compared with only children, those with two or three siblings had a lower risk of self harm. Perinatal and family composition factors have a broad influence on mental health outcomes. These data suggest that the existence of younger, as well as elder siblings may be important.

Assessing Effectiveness of a Nonhuman Animal Welfare Education Program for Primary School Children.

PubMed

Hawkins, Roxanne D; Williams, Joanne M

2017-01-01

Nonhuman animal welfare education aims to promote positive relationships between children and animals and thus improve animal welfare, yet few scientific evaluations of these programs exist. This study aimed to evaluate the effectiveness of an education program developed by the Scottish Society for the Prevention of Cruelty to Animals (SPCA) that included 4 interventions focusing on pets (companion animals), wild animals, farm animals, and general animal rescues. Knowledge, attachment to pets, and attitudes and beliefs about animal minds were assessed at pretest, posttest, and delayed posttest using a questionnaire administered to 1,217 Scottish children aged 7 to 13 years old. Results showed a significant positive impact of the program on knowledge about animals and the Scottish SPCA for all interventions. The pet and farming interventions significantly impacted children's beliefs about animal minds. There were trends toward improvements in a range of other measures. This study highlights the importance of teaching animal welfare education to children for early prevention of animal cruelty, discusses the need to base this education on theory and research to find effective change, and demonstrates how evidence-based practice can inform future education programs.

Sequence polymorphism in candidate genes for differences in winter plumage between Scottish and Scandinavian Willow Grouse (Lagopus lagopus).

PubMed

Skoglund, Pontus; Höglund, Jacob

2010-04-23

Population variation in the degree of seasonal polymorphism is rare in birds, and the genetic basis of this phenomenon remains largely undescribed. Both sexes of Scandinavian and Scottish Willow grouse (Lagopus lagopus) display marked differences in their winter phenotypes, with Scottish grouse retaining a pigmented plumage year-round and Scandinavian Willow grouse molting to a white morph during winter. A widely studied pathway implicated in vertebrate pigmentation is the melanin system, for which functional variation has been characterised in many taxa. We sequenced coding regions from four genes involved in melanin pigmentation (DCT, MC1R, TYR and TYRP1), and an additional control involved in the melanocortin pathway (AGRP), to investigate the genetic basis of winter plumage in Lagopus. Despite the well documented role of the melanin system in animal coloration, we found no plumage-associated polymorphism or evidence for selection in a total of approximately 2.6 kb analysed sequence. Our results indicate that the genetic basis of alternating between pigmented and unpigmented seasonal phenotypes is more likely explained by regulatory changes controlling the expression of these or other loci in the physiological pathway leading to pigmentation.

The first description of the complete natural history of uveal melanoma by two Scottish surgeons, Allan Burns and James Wardrop.

PubMed

Kivelä, Tero T

2018-03-01

James Wardrop (1782-1869), a young Scottish surgeon and an early ophthalmologist in Edinburgh, is credited for describing in 1809 retinoblastoma as an entity in his treatise 'Observations on Fungus Haematodes or Soft Cancer'. His treatise also reveals that Allan Burns (1781-1813), another young Scottish surgeon and anatomist, had invited Wardrop to assist in enucleating an eye from a 41-year-old Glasgow woman who, in retrospect, had a uveal melanoma. Her eye had become blind 4 months after symptoms of exudative retinal detachment had appeared, and it had become painful after a further 2-4 months. The tumour eventually perforated the sclera, and she died within a year thereafter of hepatic metastases. Burns and Wardrop went on to publish detailed parallel accounts of the symptoms, signs, ophthalmic pathology and post-mortem findings regarding the primary, recurrent and metastatic tumour. Burns may have performed the post-mortem after exhuming the body, a common occurrence in early 19th Century Scotland, a thriving hub for teaching morbid anatomy to young surgeons at the time. © 2017 Acta Ophthalmologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

Relative professional roles in antenatal care: results of a survey in Scottish rural general practice.

PubMed

Farmer, Jane; Stimpson, Paul; Tucker, Janet

2003-11-01

There is evidence of variation and some ambiguity about self-perceived relative professional roles in antenatal care in the UK. There is little information about models of antenatal care provision in UK rural areas. In rural areas, in particular, women have limited choice in accessing health care professionals or alternative primary care delivery settings. In the light of a recent review of Scottish maternity services, it is important and timely to examine models of care and interprofessional working in antenatal care in rural areas. This study explores midwives' and GPs' perceptions about their relative professional roles in remote and rural general practice in Scotland. A questionnaire survey involving all 174 Scottish remote and rural general practices (using one definition of rurality) was conducted, followed by 20 interviews. At least one professional returned a completed questionnaire from 91% of rural practices. A number of areas of dissonance were noted between GPs' and midwives' perceptions of their roles in maternity care and, given the context of service provision, these may impact upon rural patients. Findings are relevant to wider debates on extending the primary care team and strengthening inter-disciplinary working, particularly in rural areas.

Proteomics research in India: an update.

PubMed

Reddy, Panga Jaipal; Atak, Apurva; Ghantasala, Saicharan; Kumar, Saurabh; Gupta, Shabarni; Prasad, T S Keshava; Zingde, Surekha M; Srivastava, Sanjeeva

2015-09-08

After a successful completion of the Human Genome Project, deciphering the mystery surrounding the human proteome posed a major challenge. Despite not being largely involved in the Human Genome Project, the Indian scientific community contributed towards proteomic research along with the global community. Currently, more than 76 research/academic institutes and nearly 145 research labs are involved in core proteomic research across India. The Indian researchers have been major contributors in drafting the "human proteome map" along with international efforts. In addition to this, virtual proteomics labs, proteomics courses and remote triggered proteomics labs have helped to overcome the limitations of proteomics education posed due to expensive lab infrastructure. The establishment of Proteomics Society, India (PSI) has created a platform for the Indian proteomic researchers to share ideas, research collaborations and conduct annual conferences and workshops. Indian proteomic research is really moving forward with the global proteomics community in a quest to solve the mysteries of proteomics. A draft map of the human proteome enhances the enthusiasm among intellectuals to promote proteomic research in India to the world.This article is part of a Special Issue entitled: Proteomics in India. Copyright © 2015 Elsevier B.V. All rights reserved.

Quantitative proteomics in teleost fish: insights and challenges for neuroendocrine and neurotoxicology research.

PubMed

Martyniuk, Christopher J; Popesku, Jason T; Chown, Brittany; Denslow, Nancy D; Trudeau, Vance L

2012-05-01

Neuroendocrine systems integrate both extrinsic and intrinsic signals to regulate virtually all aspects of an animal's physiology. In aquatic toxicology, studies have shown that pollutants are capable of disrupting the neuroendocrine system of teleost fish, and many chemicals found in the environment can also have a neurotoxic mode of action. Omics approaches are now used to better understand cell signaling cascades underlying fish neurophysiology and the control of pituitary hormone release, in addition to identifying adverse effects of pollutants in the teleostean central nervous system. For example, both high throughput genomics and proteomic investigations of molecular signaling cascades for both neurotransmitter and nuclear receptor agonists/antagonists have been reported. This review highlights recent studies that have utilized quantitative proteomics methods such as 2D differential in-gel electrophoresis (DIGE) and isobaric tagging for relative and absolute quantitation (iTRAQ) in neuroendocrine regions and uses these examples to demonstrate the challenges of using proteomics in neuroendocrinology and neurotoxicology research. To begin to characterize the teleost neuroproteome, we functionally annotated 623 unique proteins found in the fish hypothalamus and telencephalon. These proteins have roles in biological processes that include synaptic transmission, ATP production, receptor activity, cell structure and integrity, and stress responses. The biological processes most represented by proteins detected in the teleost neuroendocrine brain included transport (8.4%), metabolic process (5.5%), and glycolysis (4.8%). We provide an example of using sub-network enrichment analysis (SNEA) to identify protein networks in the fish hypothalamus in response to dopamine receptor signaling. Dopamine signaling altered the abundance of proteins that are binding partners of microfilaments, integrins, and intermediate filaments, consistent with data suggesting dopaminergic regulation of neuronal stability and structure. Lastly, for fish neuroendocrine studies using both high-throughput genomics and proteomics, we compare gene and protein relationships in the hypothalamus and demonstrate that correlation is often poor for single time point experiments. These studies highlight the need for additional time course analyses to better understand gene-protein relationships and adverse outcome pathways. This is important if both transcriptomics and proteomics are to be used together to investigate neuroendocrine signaling pathways or as bio-monitoring tools in ecotoxicology. Copyright © 2011 Elsevier Inc. All rights reserved.

Protein-centric N-glycoproteomics analysis of membrane and plasma membrane proteins.

PubMed

Sun, Bingyun; Hood, Leroy

2014-06-06

The advent of proteomics technology has transformed our understanding of biological membranes. The challenges for studying membrane proteins have inspired the development of many analytical and bioanalytical tools, and the techniques of glycoproteomics have emerged as an effective means to enrich and characterize membrane and plasma-membrane proteomes. This Review summarizes the development of various glycoproteomics techniques to overcome the hurdles formed by the unique structures and behaviors of membrane proteins with a focus on N-glycoproteomics. Example contributions of N-glycoproteomics to the understanding of membrane biology are provided, and the areas that require future technical breakthroughs are discussed.

Genome, Proteome and Structure of a T7-Like Bacteriophage of the Kiwifruit Canker Phytopathogen Pseudomonas syringae pv. actinidiae.

PubMed

Frampton, Rebekah A; Acedo, Elena Lopez; Young, Vivienne L; Chen, Danni; Tong, Brian; Taylor, Corinda; Easingwood, Richard A; Pitman, Andrew R; Kleffmann, Torsten; Bostina, Mihnea; Fineran, Peter C

2015-06-24

Pseudomonas syringae pv. actinidiae is an economically significant pathogen responsible for severe bacterial canker of kiwifruit (Actinidia sp.). Bacteriophages infecting this phytopathogen have potential as biocontrol agents as part of an integrated approach to the management of bacterial canker, and for use as molecular tools to study this bacterium. A variety of bacteriophages were previously isolated that infect P. syringae pv. actinidiae, and their basic properties were characterized to provide a framework for formulation of these phages as biocontrol agents. Here, we have examined in more detail φPsa17, a phage with the capacity to infect a broad range of P. syringae pv. actinidiae strains and the only member of the Podoviridae in this collection. Particle morphology was visualized using cryo-electron microscopy, the genome was sequenced, and its structural proteins were analysed using shotgun proteomics. These studies demonstrated that φPsa17 has a 40,525 bp genome, is a member of the T7likevirus genus and is closely related to the pseudomonad phages φPSA2 and gh-1. Eleven structural proteins (one scaffolding) were detected by proteomics and φPsa17 has a capsid of approximately 60 nm in diameter. No genes indicative of a lysogenic lifecycle were identified, suggesting the phage is obligately lytic. These features indicate that φPsa17 may be suitable for formulation as a biocontrol agent of P. syringae pv. actinidiae.

Integrating cell biology and proteomic approaches in plants.

PubMed

Takáč, Tomáš; Šamajová, Olga; Šamaj, Jozef

2017-10-03

Significant improvements of protein extraction, separation, mass spectrometry and bioinformatics nurtured advancements of proteomics during the past years. The usefulness of proteomics in the investigation of biological problems can be enhanced by integration with other experimental methods from cell biology, genetics, biochemistry, pharmacology, molecular biology and other omics approaches including transcriptomics and metabolomics. This review aims to summarize current trends integrating cell biology and proteomics in plant science. Cell biology approaches are most frequently used in proteomic studies investigating subcellular and developmental proteomes, however, they were also employed in proteomic studies exploring abiotic and biotic stress responses, vesicular transport, cytoskeleton and protein posttranslational modifications. They are used either for detailed cellular or ultrastructural characterization of the object subjected to proteomic study, validation of proteomic results or to expand proteomic data. In this respect, a broad spectrum of methods is employed to support proteomic studies including ultrastructural electron microscopy studies, histochemical staining, immunochemical localization, in vivo imaging of fluorescently tagged proteins and visualization of protein-protein interactions. Thus, cell biological observations on fixed or living cell compartments, cells, tissues and organs are feasible, and in some cases fundamental for the validation and complementation of proteomic data. Validation of proteomic data by independent experimental methods requires development of new complementary approaches. Benefits of cell biology methods and techniques are not sufficiently highlighted in current proteomic studies. This encouraged us to review most popular cell biology methods used in proteomic studies and to evaluate their relevance and potential for proteomic data validation and enrichment of purely proteomic analyses. We also provide examples of representative studies combining proteomic and cell biology methods for various purposes. Integrating cell biology approaches with proteomic ones allow validation and better interpretation of proteomic data. Moreover, cell biology methods remarkably extend the knowledge provided by proteomic studies and might be fundamental for the functional complementation of proteomic data. This review article summarizes current literature linking proteomics with cell biology. Copyright © 2017 Elsevier B.V. All rights reserved.

Crystal Structure and Proteomics Analysis of Empty Virus-like Particles of Cowpea Mosaic Virus.

PubMed

Huynh, Nhung T; Hesketh, Emma L; Saxena, Pooja; Meshcheriakova, Yulia; Ku, You-Chan; Hoang, Linh T; Johnson, John E; Ranson, Neil A; Lomonossoff, George P; Reddy, Vijay S

2016-04-05

Empty virus-like particles (eVLPs) of Cowpea mosaic virus (CPMV) are currently being utilized as reagents in various biomedical and nanotechnology applications. Here, we report the crystal structure of CPMV eVLPs determined using X-ray crystallography at 2.3 Å resolution and compare it with previously reported cryo-electron microscopy (cryo-EM) of eVLPs and virion crystal structures. Although the X-ray and cryo-EM structures of eVLPs are mostly similar, there exist significant differences at the C terminus of the small (S) subunit. The intact C terminus of the S subunit plays a critical role in enabling the efficient assembly of CPMV virions and eVLPs, but undergoes proteolysis after particle formation. In addition, we report the results of mass spectrometry-based proteomics analysis of coat protein subunits from CPMV eVLPs and virions that identify the C termini of S subunits undergo proteolytic cleavages at multiple sites instead of a single cleavage site as previously observed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Regulation of T-cell receptor signalling by membrane microdomains

PubMed Central

Razzaq, Tahir M; Ozegbe, Patricia; Jury, Elizabeth C; Sembi, Phupinder; Blackwell, Nathan M; Kabouridis, Panagiotis S

2004-01-01

There is now considerable evidence suggesting that the plasma membrane of mammalian cells is compartmentalized by functional lipid raft microdomains. These structures are assemblies of specialized lipids and proteins and have been implicated in diverse biological functions. Analysis of their protein content using proteomics and other methods revealed enrichment of signalling proteins, suggesting a role for these domains in intracellular signalling. In T lymphocytes, structure/function experiments and complementary pharmacological studies have shown that raft microdomains control the localization and function of proteins which are components of signalling pathways regulated by the T-cell antigen receptor (TCR). Based on these studies, a model for TCR phosphorylation in lipid rafts is presented. However, despite substantial progress in the field, critical questions remain. For example, it is unclear if membrane rafts represent a homogeneous population and if their structure is modified upon TCR stimulation. In the future, proteomics and the parallel development of complementary analytical methods will undoubtedly contribute in further delineating the role of lipid rafts in signal transduction mechanisms. PMID:15554919

Complete fold annotation of the human proteome using a novel structural feature space

DOE PAGES

Middleton, Sarah A.; Illuminati, Joseph; Kim, Junhyong

2017-04-13

Recognition of protein structural fold is the starting point for many structure prediction tools and protein function inference. Fold prediction is computationally demanding and recognizing novel folds is difficult such that the majority of proteins have not been annotated for fold classification. Here we describe a new machine learning approach using a novel feature space that can be used for accurate recognition of all 1,221 currently known folds and inference of unknown novel folds. We show that our method achieves better than 94% accuracy even when many folds have only one training example. We demonstrate the utility of this methodmore » by predicting the folds of 34,330 human protein domains and showing that these predictions can yield useful insights into potential biological function, such as prediction of RNA-binding ability. Finally, our method can be applied to de novo fold prediction of entire proteomes and identify candidate novel fold families.« less

Effect of posttranslational modifications on enzyme function and assembly.

PubMed

Ryšlavá, Helena; Doubnerová, Veronika; Kavan, Daniel; Vaněk, Ondřej

2013-10-30

The detailed examination of enzyme molecules by mass spectrometry and other techniques continues to identify hundreds of distinct PTMs. Recently, global analyses of enzymes using methods of contemporary proteomics revealed widespread distribution of PTMs on many key enzymes distributed in all cellular compartments. Critically, patterns of multiple enzymatic and nonenzymatic PTMs within a single enzyme are now functionally evaluated providing a holistic picture of a macromolecule interacting with low molecular mass compounds, some of them being substrates, enzyme regulators, or activated precursors for enzymatic and nonenzymatic PTMs. Multiple PTMs within a single enzyme molecule and their mutual interplays are critical for the regulation of catalytic activity. Full understanding of this regulation will require detailed structural investigation of enzymes, their structural analogs, and their complexes. Further, proteomics is now integrated with molecular genetics, transcriptomics, and other areas leading to systems biology strategies. These allow the functional interrogation of complex enzymatic networks in their natural environment. In the future, one might envisage the use of robust high throughput analytical techniques that will be able to detect multiple PTMs on a global scale of individual proteomes from a number of carefully selected cells and cellular compartments. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine. Copyright © 2013 Elsevier B.V. All rights reserved.

Gas-Phase Enrichment of Multiply Charged Peptide Ions by Differential Ion Mobility Extend the Comprehensiveness of SUMO Proteome Analyses

NASA Astrophysics Data System (ADS)

Pfammatter, Sibylle; Bonneil, Eric; McManus, Francis P.; Thibault, Pierre

2018-04-01

The small ubiquitin-like modifier (SUMO) is a member of the family of ubiquitin-like modifiers (UBLs) and is involved in important cellular processes, including DNA damage response, meiosis and cellular trafficking. The large-scale identification of SUMO peptides in a site-specific manner is challenging not only because of the low abundance and dynamic nature of this modification, but also due to the branched structure of the corresponding peptides that further complicate their identification using conventional search engines. Here, we exploited the unusual structure of SUMO peptides to facilitate their separation by high-field asymmetric waveform ion mobility spectrometry (FAIMS) and increase the coverage of SUMO proteome analysis. Upon trypsin digestion, branched peptides contain a SUMO remnant side chain and predominantly form triply protonated ions that facilitate their gas-phase separation using FAIMS. We evaluated the mobility characteristics of synthetic SUMO peptides and further demonstrated the application of FAIMS to profile the changes in protein SUMOylation of HEK293 cells following heat shock, a condition known to affect this modification. FAIMS typically provided a 10-fold improvement of detection limit of SUMO peptides, and enabled a 36% increase in SUMO proteome coverage compared to the same LC-MS/MS analyses performed without FAIMS. [Figure not available: see fulltext.

Comparative Analysis of Proteomes and Functionomes Provides Insights into Origins of Cellular Diversification

PubMed Central

Caetano-Anollés, Gustavo

2013-01-01

Reconstructing the evolutionary history of modern species is a difficult problem complicated by the conceptual and technical limitations of phylogenetic tree building methods. Here, we propose a comparative proteomic and functionomic inferential framework for genome evolution that allows resolving the tripartite division of cells and sketching their history. Evolutionary inferences were derived from the spread of conserved molecular features, such as molecular structures and functions, in the proteomes and functionomes of contemporary organisms. Patterns of use and reuse of these traits yielded significant insights into the origins of cellular diversification. Results uncovered an unprecedented strong evolutionary association between Bacteria and Eukarya while revealing marked evolutionary reductive tendencies in the archaeal genomic repertoires. The effects of nonvertical evolutionary processes (e.g., HGT, convergent evolution) were found to be limited while reductive evolution and molecular innovation appeared to be prevalent during the evolution of cells. Our study revealed a strong vertical trace in the history of proteins and associated molecular functions, which was reliably recovered using the comparative genomics approach. The trace supported the existence of a stem line of descent and the very early appearance of Archaea as a diversified superkingdom, but failed to uncover a hidden canonical pattern in which Bacteria was the first superkingdom to deploy superkingdom-specific structures and functions. PMID:24492748

Automated Interpretation of Subcellular Patterns in Fluorescence Microscope Images for Location Proteomics

PubMed Central

Chen, Xiang; Velliste, Meel; Murphy, Robert F.

2010-01-01

Proteomics, the large scale identification and characterization of many or all proteins expressed in a given cell type, has become a major area of biological research. In addition to information on protein sequence, structure and expression levels, knowledge of a protein’s subcellular location is essential to a complete understanding of its functions. Currently subcellular location patterns are routinely determined by visual inspection of fluorescence microscope images. We review here research aimed at creating systems for automated, systematic determination of location. These employ numerical feature extraction from images, feature reduction to identify the most useful features, and various supervised learning (classification) and unsupervised learning (clustering) methods. These methods have been shown to perform significantly better than human interpretation of the same images. When coupled with technologies for tagging large numbers of proteins and high-throughput microscope systems, the computational methods reviewed here enable the new subfield of location proteomics. This subfield will make critical contributions in two related areas. First, it will provide structured, high-resolution information on location to enable Systems Biology efforts to simulate cell behavior from the gene level on up. Second, it will provide tools for Cytomics projects aimed at characterizing the behaviors of all cell types before, during and after the onset of various diseases. PMID:16752421

Quantitative Proteomic Profiling of Low-Dose Ionizing Radiation Effects in a Human Skin Model

PubMed Central

Hengel, Shawna M.; Aldrich, Joshua T.; Waters, Katrina M.; Pasa-Tolic, Ljiljana; Stenoien, David L.

2014-01-01

To assess responses to low-dose ionizing radiation (LD-IR) exposures potentially encountered during medical diagnostic procedures, nuclear accidents or terrorist acts, a quantitative proteomic approach was used to identify changes in protein abundance in a reconstituted human skin tissue model treated with 0.1 Gy of ionizing radiation. To improve the dynamic range of the assay, subcellular fractionation was employed to remove highly abundant structural proteins and to provide insight into radiation-induced alterations in protein localization. Relative peptide quantification across cellular fractions, control and irradiated samples was performing using 8-plex iTRAQ labeling followed by online two-dimensional nano-scale liquid chromatography and high resolution MS/MS analysis. A total of 107 proteins were detected with statistically significant radiation-induced change in abundance (>1.5 fold) and/or subcellular localization compared to controls. The top biological pathways identified using bioinformatics include organ development, anatomical structure formation and the regulation of actin cytoskeleton. From the proteomic data, a change in proteolytic processing and subcellular localization of the skin barrier protein, filaggrin, was identified, and the results were confirmed by western blotting. This data indicate post-transcriptional regulation of protein abundance, localization and proteolytic processing playing an important role in regulating radiation response in human tissues. PMID:28250387

DIGE Proteome Analysis Reveals Suitability of Ischemic Cardiac In Vitro Model for Studying Cellular Response to Acute Ischemia and Regeneration

PubMed Central

Haas, Sina; Jahnke, Heinz-Georg; Moerbt, Nora; von Bergen, Martin; Aharinejad, Seyedhossein; Andrukhova, Olena; Robitzki, Andrea A.

2012-01-01

Proteomic analysis of myocardial tissue from patient population is suited to yield insights into cellular and molecular mechanisms taking place in cardiovascular diseases. However, it has been limited by small sized biopsies and complicated by high variances between patients. Therefore, there is a high demand for suitable model systems with the capability to simulate ischemic and cardiotoxic effects in vitro, under defined conditions. In this context, we established an in vitro ischemia/reperfusion cardiac disease model based on the contractile HL-1 cell line. To identify pathways involved in the cellular alterations induced by ischemia and thereby defining disease-specific biomarkers and potential target structures for new drug candidates we used fluorescence 2D-difference gel electrophoresis. By comparing spot density changes in ischemic and reperfusion samples we detected several protein spots that were differentially abundant. Using MALDI-TOF/TOF-MS and ESI-MS the proteins were identified and subsequently grouped by functionality. Most prominent were changes in apoptosis signalling, cell structure and energy-metabolism. Alterations were confirmed by analysis of human biopsies from patients with ischemic cardiomyopathy. With the establishment of our in vitro disease model for ischemia injury target identification via proteomic research becomes independent from rare human material and will create new possibilities in cardiac research. PMID:22384053

Effect of greenhouse conditions on the leaf apoplastic proteome of Coffea arabica plants.

PubMed

Guerra-Guimarães, Leonor; Vieira, Ana; Chaves, Inês; Pinheiro, Carla; Queiroz, Vagner; Renaut, Jenny; Ricardo, Cândido P

2014-06-02

This work describes the coffee leaf apoplastic proteome and its modulation by the greenhouse conditions. The apoplastic fluid (APF) was obtained by leaf vacuum infiltration, and the recovered proteins were separated by 2-DE and subsequently identified by matrix assisted laser desorption/ionization time of flight-mass spectrometry, followed by homology search in EST coffee databases. Prediction tools revealed that the majority of the 195 identified proteins are involved in cell wall metabolism and in stress/defense responses. Although most of the proteins follow the classical secretory mechanism, a low percentage of them seem to result from unconventional secretion (leaderless secreted proteins). Principal components analysis revealed that the APF samples formed two distinct groups, with the temperature amplitude mostly contributing for this separation (higher or lower than 10°C, respectively). Sixty one polypeptide spots allowed defining these two groups and 28 proteins were identified, belonging to carbohydrate metabolism, cell wall modification and proteolysis. Interestingly stress/defense proteins appeared as more abundant in Group I which is associated with a higher temperature amplitude. It seems that the proteins in the coffee leaf APF might be implicated in structural modifications in the extracellular space that are crucial for plant development/adaptation to the conditions of the prevailing environment. This is the first detailed proteomic study of the coffee leaf apoplastic fluid (APF) and of its modulation by the greenhouse conditions. The comprehensive overview of the most abundant proteins present in the extra-cellular compartment is particularly important for the understanding of coffee responses to abiotic/biotic stress. This article is part of a Special Issue entitled: Environmental and structural proteomics. Copyright © 2014 Elsevier B.V. All rights reserved.

Comparative proteomic profiling of the choline transporter-like1 (CHER1) mutant provides insights into plasmodesmata composition of fully developed Arabidopsis thaliana leaves.

PubMed

Kraner, Max E; Müller, Carmen; Sonnewald, Uwe

2017-11-01

In plants, intercellular communication and exchange are highly dependent on cell wall bridging structures between adhering cells, so-called plasmodesmata (PD). In our previous genetic screen for PD-deficient Arabidopsis mutants, we described choline transporter-like 1 (CHER1) being important for PD genesis and maturation. Leaves of cher1 mutant plants have up to 10 times less PD, which do not develop to complex structures. Here we utilize the T-DNA insertion mutant cher1-4 and report a deep comparative proteomic workflow for the identification of cell-wall-embedded PD-associated proteins. Analyzing triplicates of cell-wall-enriched fractions in depth by fractionation and quantitative high-resolution mass spectrometry, we compared > 5000 proteins obtained from fully developed leaves. Comparative data analysis and subsequent filtering generated a list of 61 proteins being significantly more abundant in Col-0. This list was enriched for previously described PD-associated proteins. To validate PD association of so far uncharacterized proteins, subcellular localization analyses were carried out by confocal laser-scanning microscopy. This study confirmed the association of PD for three out of four selected candidates, indicating that the comparative approach indeed allowed identification of so far undescribed PD-associated proteins. Performing comparative cell wall proteomics of Nicotiana benthamiana tissue, we observed an increase in abundance of these three selected candidates during sink to source transition. Taken together, our comparative proteomic approach revealed a valuable data set of potential PD-associated proteins, which can be used as a resource to unravel the molecular composition of complex PD and to investigate their function in cell-to-cell communication. © 2017 The Authors. The Plant Journal published by John Wiley & Sons Ltd and Society for Experimental Biology.

Protein differences between human trapezius and vastus lateralis muscles determined with a proteomic approach.

PubMed

Hadrévi, Jenny; Hellström, Fredrik; Kieselbach, Thomas; Malm, Christer; Pedrosa-Domellöf, Fatima

2011-08-10

The trapezius muscle is a neck muscle that is susceptible to chronic pain conditions associated with repetitive tasks, commonly referred to as chronic work-related myalgia, hence making the trapezius a muscle of clinical interest. To provide a basis for further investigations of the proteomic traits of the trapezius muscle in disease, two-dimensional difference gel electrophoresis (2D-DIGE) was performed on the healthy trapezius using vastus lateralis as a reference. To obtain as much information as possible from the vast proteomic data set, both one-way ANOVA, with and without false discovery rate (FDR) correlation, and partial least square projection to latent structures with discriminant analysis (PLS-DA) were combined to compare the outcome of the analysis. The trapezius and vastus lateralis showed significant differences in metabolic, contractile and regulatory proteins, with different results depending on choice of statistical approach and pre-processing technique. Using the standard method, FDR correlated one-way ANOVA, 42 protein spots differed significantly in abundance between the two muscles. Complementary analysis using immunohistochemistry and western blot confirmed the results from the 2D-DIGE analysis. The proteomic approach used in the present study combining 2D-DIGE and multivariate modelling provided a more comprehensive comparison of the protein profiles of the human trapezius and vastus lateralis muscle, than previously possible to obtain with immunohistochemistry or SDS-PAGE alone. Although 2D-DIGE has inherent limitations it is particularly useful to comprehensively screen for important structural and metabolic proteins, and appears to be a promising tool for future studies of patients suffering from chronic work related myalgia or other muscle diseases.

Domain selection combined with improved cloning strategy for high throughput expression of higher eukaryotic proteins

PubMed Central

Chen, Yunjia; Qiu, Shihong; Luan, Chi-Hao; Luo, Ming

2007-01-01

Background Expression of higher eukaryotic genes as soluble, stable recombinant proteins is still a bottleneck step in biochemical and structural studies of novel proteins today. Correct identification of stable domains/fragments within the open reading frame (ORF), combined with proper cloning strategies, can greatly enhance the success rate when higher eukaryotic proteins are expressed as these domains/fragments. Furthermore, a HTP cloning pipeline incorporated with bioinformatics domain/fragment selection methods will be beneficial to studies of structure and function genomics/proteomics. Results With bioinformatics tools, we developed a domain/domain boundary prediction (DDBP) method, which was trained by available experimental data. Combined with an improved cloning strategy, DDBP had been applied to 57 proteins from C. elegans. Expression and purification results showed there was a 10-fold increase in terms of obtaining purified proteins. Based on the DDBP method, the improved GATEWAY cloning strategy and a robotic platform, we constructed a high throughput (HTP) cloning pipeline, including PCR primer design, PCR, BP reaction, transformation, plating, colony picking and entry clones extraction, which have been successfully applied to 90 C. elegans genes, 88 Brucella genes, and 188 human genes. More than 97% of the targeted genes were obtained as entry clones. This pipeline has a modular design and can adopt different operations for a variety of cloning/expression strategies. Conclusion The DDBP method and improved cloning strategy were satisfactory. The cloning pipeline, combined with our recombinant protein HTP expression pipeline and the crystal screening robots, constitutes a complete platform for structure genomics/proteomics. This platform will increase the success rate of purification and crystallization dramatically and promote the further advancement of structure genomics/proteomics. PMID:17663785

Completed | Office of Cancer Clinical Proteomics Research

Cancer.gov

Prior to the current Clinical Proteomic Tumor Analysis Consortium (CPTAC), previously funded initiatives associated with clinical proteomics research included: Clinical Proteomic Tumor Analysis Consortium (CPTAC 2.0) Clinical Proteomic Technologies for Cancer Initiative (CPTC) Mouse Proteomic Technologies Initiative

Mutuality, empowerment and the health-wealth model: the Scottish context.

PubMed

Howieson, Brian

2013-06-01

This paper will offer an alternative paradigm to healthcare delivery by introducing the concept of mutuality and empowerment into the existing health-wealth model. The backdrop is provided by Better Health, Better Care (Scottish Government 2007), Section 1 of which is entitled 'Towards a Mutual NHS'. In detail, the paper will: revisit what is meant by mutuality; advance the meaning of the 'public interest'; explore empowerment and community empowerment and its relationship to health; and introduce a model, which tries to link these concepts and terms together. It is hoped that this analysis will help researchers and practitioners alike further appreciate the important concept of mutuality and empowerment into the existing health-wealth model.

The manufacture of blood plasma products in Scotland: a brief history.

PubMed

Foster, Peter R

2016-02-01

A number of essential clinical products are derived from human blood plasma, including immunoglobulin products for the treatment of infections and disorders of immunity; albumin for protein and fluid replacement and coagulation factors for the treatment of haemophilia and other disorders of haemostasis. For many years, these protein pharmaceuticals were manufactured by the Scottish National Blood Transfusion Service (SNBTS) at its Scottish Protein Fractionation Centre (PFC) in Edinburgh, a contribution which ended with the closure of the PFC in 2008. The origins and development of plasma fractionation in Scotland are summarised in this article, as well as issues which contributed to the closure of the PFC. © The Author(s) 2015.