Genetics of Hereditary Ataxia in Scottish Terriers.

Science.gov (United States)

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.

Progress with the Scottish Trading Arrangements Group (STAG)

International Nuclear Information System (INIS)

Fellows, A.

1998-01-01

Since November 1996 STAG has operated as a forum to allow traders in the Scottish market to consider trading arrangements which will facilitate competition while coping with foreseeable trading requirements beyond the 1998 franchise break. The author has promoted the interest of renewables generators on behalf of the Scottish Renewables Forum throughout this process. An Interim Report summarising the high level options considered was submitted to OFFER in June 1997. This paper summarises the interim report content and draws on other aspects of the Scottish market to review the future prospects in Scotland for trading electricity form wind energy schemes. (Author)

The Scottish Independence Referendum and After

Directory of Open Access Journals (Sweden)

Michael Keating

2015-04-01

Full Text Available The Scottish independence referendum on 18 September 2014 produced an apparently decisive result, with 45 per cent for independence and 55 per cent against. Yet, it has not settled the constitutional issue. There was a huge public engagement in the campaign, which has left a legacy for Scottish and UK politics. Scotland has been reinforced as a political community. The losing Yes side has emerged in better shape and more optimistic, while the winners have struggled to formulate the better autonomy package they had promised. Public opinion continues to favour maximum devolution short of independence. Scotland is a case of the kind of spatial rescaling that is taking place more generally across Europe, as new forms of statehood and of sovereignty evolve. Scottish public opinion favours more self-government but no longer recognizes the traditional nation-state model presented in the referendum question.

Structural Proteomics of Herpesviruses

Science.gov (United States)

Leroy, Baptiste; Gillet, Laurent; Vanderplasschen, Alain; Wattiez, Ruddy

2016-01-01

Herpesviruses are highly prevalent viruses associated with numerous pathologies both in animal and human populations. Until now, most of the strategies used to prevent or to cure these infections have been unsuccessful because these viruses have developed numerous immune evasion mechanisms. Therefore, a better understanding of their complex lifecycle is needed. In particular, while the genome of numerous herpesviruses has been sequenced, the exact composition of virions remains unknown for most of them. Mass spectrometry has recently emerged as a central method and has permitted fundamental discoveries in virology. Here, we review mass spectrometry-based approaches that have recently allowed a better understanding of the composition of the herpesvirus virion. In particular, we describe strategies commonly used for proper sample preparation and fractionation to allow protein localization inside the particle but also to avoid contamination by nonstructural proteins. A collection of other important data regarding post-translational modifications or the relative abundance of structural proteins is also described. This review also discusses the poorly studied importance of host proteins in herpesvirus structural proteins and the necessity to develop a quantitative workflow to better understand the dynamics of the structural proteome. In the future, we hope that this collaborative effort will assist in the development of new strategies to fight these infections. PMID:26907323

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

Science.gov (United States)

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.

Scottish Nuclear, the company

International Nuclear Information System (INIS)

Yeomans, R.M.

1991-01-01

A former chief executive of Scottish Nuclear, formed when United Kingdom electricity generation was privatized, describes the financial viability of the company and considers the future of nuclear power. Scottish Nuclear owns and operates the Advanced Gas Cooled (AGR) and Magnox reactors at Hunterston and the AGR reactor at Torness and is a separate company from those dealing with hydro-electric and non-nuclear generation of electricity. Costs of running the reactors is identified as a proportion of the whole for certain key issues such as station costs, depreciation, decommissioning and insurance. While nuclear power generation using outmoded Magnox reactors is costly, the ecological cost of global warming is seen as more of a problem. Future policy for nuclear power in Scotland must include new plant, probably pressurized water reactors and a clear policy of safety enhancement. (UK)

Education in the Scottish Parliament: Parliamentary Report Number 3.

Science.gov (United States)

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,…

Testing the social identity relative deprivation (SIRD) model of social change: the political rise of Scottish nationalism.

Science.gov (United States)

Abrams, Dominic; Grant, Peter R

2012-12-01

We tested a social-identity relative deprivation (SIRD) model predicting Scottish nationalist beliefs and intention to vote for the separatist Scottish Nationalist Party (SNP). Data were from a survey of a large and representative sample of Scottish teenagers administered in the late 1980s. The SIRD model distinguishes effects of group-based and personal relative deprivation, which should be independent of one another. Importantly, social change beliefs should mediate the effects of both collective relative deprivation and group identification on protest intentions (in this case intention to vote for the SNP). Egoistic relative deprivation should be the strongest predictor of feelings of depression. Using structural equation modelling, the results strongly support this model and replicate in two different cohorts. ©2011 The British Psychological Society.

Wear Fast, Die Young: More Worn Teeth and Shorter Lives in Iberian Compared to Scottish Red Deer.

Science.gov (United States)

Pérez-Barbería, F J; Carranza, J; Sánchez-Prieto, C

2015-01-01

Teeth in Cervidae are permanent structures that are not replaceable or repairable; consequently their rate of wear, due to the grinding effect of food and dental attrition, affects their duration and can determine an animal's lifespan. Tooth wear is also a useful indicator of accumulative life energy investment in intake and mastication and their interactions with diet. Little is known regarding how natural and sexual selection operate on dental structures within a species in contrasting environments and how these relate to life history traits to explain differences in population rates of tooth wear and longevity. We hypothesised that populations under harsh environmental conditions should be selected for more hypsodont teeth while sexual selection may maintain similar sex differences within different populations. We investigated the patterns of tooth wear in males and females of Iberian red deer (Cervus elaphus hispanicus) in Southern Spain and Scottish red deer (C. e. scoticus) across Scotland, that occur in very different environments, using 10343 samples from legal hunting activities. We found higher rates of both incisor and molar wear in the Spanish compared to Scottish populations. However, Scottish red deer had larger incisors at emergence than Iberian red deer, whilst molars emerged at a similar size in both populations and sexes. Iberian and Scottish males had earlier tooth depletion than females, in support of a similar sexual selection process in both populations. However, whilst average lifespan for Iberian males was 4 years shorter than that for Iberian females and Scottish males, Scottish males only showed a reduction of 1 year in average lifespan with respect to Scottish females. More worn molars were associated with larger mandibles in both populations, suggesting that higher intake and/or greater investment in food comminution may have favoured increased body growth, before later loss of tooth efficiency due to severe wear. These results

The engineering function in Scottish Nuclear

International Nuclear Information System (INIS)

Grant, J.

1991-01-01

The work of the Engineering and Development Division of Scottish Nuclear is described in this article. This company, formed since the privatization of electricity generation in the United Kingdom, owns and operates the two Hunterston Magnox reactors and the Torness Advanced Gass Cooled Reactors. Principle responsibilities such as maintaining safety standards, formulating policy for radioactive waste disposal and decommissioning and optimally controlling the nuclear generation cycle are outlined. Objectives for the next five years are identified and explained separately. The experience, knowledge and expertise of engineering staff is stressed as being of key importance to the future success of Scottish Nuclear. (UK)

Fresh Air Practices in English and Scottish Homes

DEFF Research Database (Denmark)

Hauge, Bettina

2013-01-01

This article presents anthropological research results on how and why English and Scottish families use the fresh air from outside into the home (FAFOH). The introducing exchange was often heard in the English and Scottish families visited. Throughout the entire study the opposite only occurred...... in a few cases: The man opening the window, the woman closing it, in her own words: ”so that I stay snug”....

Scottish Stroke Research Network: the first three years.

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Annual report and accounts 1994/95: Scottish Nuclear

International Nuclear Information System (INIS)

1995-01-01

The Annual Report and Accounts for Scottish Nuclear are presented for the year 1994/1995. Scottish Nuclear Limited produces about half of Scotland's electricity requirement in its advanced gas-cooled reactors (AGRs) at Hunterston and Torness. It also has responsibility for decommissioning the Hunterston A Magnox nuclear power station. The role of the company in the international arena and as part of the United Kingdom's electric power industry, following privatisation, are discussed. (UK)

“The tie that binds”: commerce, migration, and the Australian Scottish delegation of 1928

Directory of Open Access Journals (Sweden)

Benjamin Vincent Wilkie

2014-10-01

Full Text Available By examining the commercial and migratory connections forged between Australia and Scotland between the wars, this article extends discussions of the relationship between the Empire and the Scottish diaspora in Australia. Foreign trade and investment was central to Scotland’s role in the British Empire, and Scottish commercial activities in Australia had their own unique contexts and outcomes. The Australian Scottish Delegation of 1928 offers a distinct example of the commercial links forged between Australia and Scotland in the context of the Empire, and presents insights into the way in which Scottish émigrés imagined their role in the imperial project. Additionally, the linkage of economic development and migration during the interwar period took on a distinctive Scottish flavour with the delegation, and the selection of migrants for emigration offers insights into the ways in which delegates defined and understood the Scottish diaspora in Australia.

Educational Theory and the Social Vision of the Scottish Enlightenment

Science.gov (United States)

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…

Mining the granule proteome

DEFF Research Database (Denmark)

Albrethsen, Jakob; Goetze, Jens P; Johnsen, Anders H

2015-01-01

Proteomics of secretory granules is an emerging strategy for identifying secreted proteins, including potentially novel candidate biomarkers and peptide hormones. In addition, proteomics can provide information about the abundance, localization and structure (post-translational modification) of g...

Proteomics of Maize Root Development.

Science.gov (United States)

Hochholdinger, Frank; Marcon, Caroline; Baldauf, Jutta A; Yu, Peng; Frey, Felix P

2018-01-01

Maize forms a complex root system with structurally and functionally diverse root types that are formed at different developmental stages to extract water and mineral nutrients from soil. In recent years proteomics has been intensively applied to identify proteins involved in shaping the three-dimensional architecture and regulating the function of the maize root system. With the help of developmental mutants, proteomic changes during the initiation and emergence of shoot-borne, lateral and seminal roots have been examined. Furthermore, root hairs were surveyed to understand the proteomic changes during the elongation of these single cell type structures. In addition, primary roots have been used to study developmental changes of the proteome but also to investigate the proteomes of distinct tissues such as the meristematic zone, the elongation zone as well as stele and cortex of the differentiation zone. Moreover, subcellular fractions of the primary root including cell walls, plasma membranes and secreted mucilage have been analyzed. Finally, the superior vigor of hybrid seedling roots compared to their parental inbred lines was studied on the proteome level. In summary, these studies provide novel insights into the complex proteomic interactions of the elaborate maize root system during development.

Proteomics of Maize Root Development

Directory of Open Access Journals (Sweden)

Frank Hochholdinger

2018-03-01

Full Text Available Maize forms a complex root system with structurally and functionally diverse root types that are formed at different developmental stages to extract water and mineral nutrients from soil. In recent years proteomics has been intensively applied to identify proteins involved in shaping the three-dimensional architecture and regulating the function of the maize root system. With the help of developmental mutants, proteomic changes during the initiation and emergence of shoot-borne, lateral and seminal roots have been examined. Furthermore, root hairs were surveyed to understand the proteomic changes during the elongation of these single cell type structures. In addition, primary roots have been used to study developmental changes of the proteome but also to investigate the proteomes of distinct tissues such as the meristematic zone, the elongation zone as well as stele and cortex of the differentiation zone. Moreover, subcellular fractions of the primary root including cell walls, plasma membranes and secreted mucilage have been analyzed. Finally, the superior vigor of hybrid seedling roots compared to their parental inbred lines was studied on the proteome level. In summary, these studies provide novel insights into the complex proteomic interactions of the elaborate maize root system during development.

Characterization of viruses infecting potato plants from a single location in Shetland, an isolated scottish archipelago

DEFF Research Database (Denmark)

Mortensen, R.J.; Shen, Xinyi; Reid, Alex

2010-01-01

, as were 29 Scottish mainland isolates of the same four potato virus species, and these 58 isolates were compared to previously published sequence data. This has allowed the characterization of viruses from a relatively isolated location, where there is little production of ware potatoes and no seed potato...... production. Phylogenetic homogeneity of the Shetland isolates of PVS and PVV was apparent. PVX was more heterogeneous, and Shetland isolates cluster with the Scottish isolates in a group which includes Asian and European isolates. For PVA, the majority of the Shetland and Scottish mainland isolates formed...... a predominantly Scottish grouping, with the remaining Shetland and Scottish mainland isolates clustering with a previously characterized Scottish isolate. There were three main groups of PVA, of which the Scottish grouping was the only one which did not have a fully characterized representative. To extend...

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

Science.gov (United States)

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.

Renewable energy and Scottish trading arrangements

International Nuclear Information System (INIS)

2001-01-01

This report summarises the findings of a project involving the participation of the Scottish Renewables Forum (SRF) in the ongoing Ofgem consultation process concerning the future electricity trading arrangements in Scotland. The present administrative arrangements, the activities of the SRF, the prospects for the British Electricity Trading and Transmission Arrangements (BETTA), generator connection policy, and transmission access are discussed, and an overview of consultations relating to Scotland-England interconnection access is presented. The appendices cover the SRF responses to the Ofgem consultation, a discussion paper in advance of the SRF meeting with Ofgem in April 2001, an SRF trading update, the SRF's responses to Ofgem's Environmental Action Plan, the Scottish Embedded Generators Working Group's terms of reference and draft paper on issues, and a briefing on prices in administered arrangements

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

Science.gov (United States)

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

Science.gov (United States)

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…

[Methods of quantitative proteomics].

Science.gov (United States)

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.

The Redox Proteome*

Science.gov (United States)

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

Operating experience at Scottish Nuclear's power stations

International Nuclear Information System (INIS)

Blackburn, P.

1991-01-01

A brief history is presented of the design and operation of the four Scottish nuclear power stations currently run by Scottish Nuclear, namely Hunterston 'A' and 'B' and the Torness reactors. A design flaw in the Magnox reactor at Hunterston 'A' led to it being operated at lower than optimal temperature and hence producing less power. For Hunterston 'B' reactor the Advanced Gas Cooled design prototype was used. Operating setbacks and successes are noted. The design chosen for Torness embraced all the good points of Hunterston 'B' but sought to eliminate its faults. After 26 years of successful operation Hunterston 'A' is now being decommissioned, while the other three stations continue to generate electricity successfully. (UK)

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

Science.gov (United States)

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…

Does Scottish Education Need Traditions?

Science.gov (United States)

Paterson, Lindsay

2009-01-01

Scottish education was, until quite recently, the conscious product of liberal tradition, of the belief by influential elites that the nation's educational history was strong, coherent, and progressive, a source of economic flexibility, of modernising ideas, and of liberal opportunity. In recent decades, however, it has become fashionable to decry…

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

Science.gov (United States)

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.

Cashmere production from Scottish Cashmere kids and crossbreed Scottish Cashmere x Jonica kids

Directory of Open Access Journals (Sweden)

Giuseppe Marsico

2010-01-01

Full Text Available This study is part of a much wider research programme to evaluate the possibility of producing valuable textile fibres, such as cashmere, from goat breeds reared in Italy. In order to achieve this, we have used crossbreeding. The first stage of the programme consisted of evaluating cashmere production in F1 kids obtained by crossing white-haired Jonica does, which have no secondary fibres, with Scottish Cashmere bucks. The trial lasted one year starting in March 2007, and took place in the Department of Animal Production of the University of Bari (Italy. We used 14 male kids: 7 Scottish Cashmere (SC group, and 7 F1 (SC x J group derived from crossing Scottish Cashmere bucks with does of the Jonica breed, commonly reared in southern Italy. All the parameters considered (live weight, number and active percentage of primary and secondary follicles, S/P ratio, patch weight, growth and length of guard hair and down, yield, down production and diameter, blood protein and T3 and T4 were significantly influenced (P<0.01 by age. Genotype also had a significant effect (P<0.01 on all parameters except for the active percentage of primary follicles and the blood protein level. The factors which influence down production showed the heterosis effect to a varying extent in F1, but they still produced significantly less than the SC group kids (38.5±4.04 vs 68.5±9.16 g; P<0.01. These results are largely due to both their low number of secondary follicles (30.0±1.46 vs 39.3±1.02; P<0.01, which also have a lower percentage of activity (64.7±2.47 vs 90.0±1.53; P<0.01, and also to the down length which was 28% shorter than in SC group. This genetic combination is clearly unsatisfactory so others must be sought, probably by using more rustic local breeds, as well as more productive breeds for crossbreeding.

Personality structure in the domestic cat (Felis silvestris catus), Scottish wildcat (Felis silvestris grampia), clouded leopard (Neofelis nebulosa), snow leopard (Panthera uncia), and African lion (Panthera leo): a comparative study.

Science.gov (United States)

Gartner, Marieke Cassia; Powell, David M; Weiss, Alexander

2014-11-01

Although the study of nonhuman personality has increased in the last decade, there are still few studies on felid species, and the majority focus on domestic cats. We assessed the structure of personality and its reliability in five felids-domestic cats, clouded leopards, snow leopards, African lions, and previous data on Scottish wildcats-and compared the results. In addition to the benefits of understanding more about this taxon, comparative studies of personality structure have the potential to provide information on evolutionary relationships among closely related species. Each of the species studied was found to have three factors of personality. Scottish wildcats' factors were labeled Dominance, Agreeableness, and Self Control; domestic cats' factors were Dominance, Impulsiveness, and Neuroticism; clouded leopards' factors were Dominance/Impulsiveness, Agreeableness/Openness, and Neuroticism; snow leopards' factors were Dominance, Impulsiveness/Openness, and Neuroticism; and African lions' factors were Dominance, Impulsiveness, and Neuroticism. The Neuroticism and Impulsiveness factors were similar, as were two of the Dominance factors. A taxon-level personality structure also showed three similar factors. Age and sex effects are also discussed. (PsycINFO Database Record (c) 2014 APA, all rights reserved).

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

Science.gov (United States)

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 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.

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

Science.gov (United States)

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.

The Scottish Enlightenment and Its Influence on the American Enlightenment

OpenAIRE

Tanaka, Hideo

2010-01-01

It is often said that Witherspoon brought Scottish Enlightenment to America, and diffused Reid’s Common Sense Philosophy in the continent. At the time he arrived in the former British colony, however, the Americans had already read Scottish books, such as those written by Hutcheson, Hume, Kames, Montesquieu, Locke, Cato, and others. Hutcheson’s Introduction had been used as a text book in Harvard and elsewhere. America’s struggle for independence had appealed to the right of resistance agains...

Using the SIRDE model of social change to examine the vote of Scottish teenagers in the 2014 independence referendum.

Science.gov (United States)

Grant, Peter R; Bennett, Mark; Abrams, Dominic

2017-09-01

Five hundred and seventy-three Scottish high school students were surveyed in the 2 months following the 2014 referendum on Scotland's independence. We used the Social Identity, Relative Deprivation, collective Efficacy (SIRDE) model of social change to examine the social psychological factors that should have influenced the voting choices of these teenagers. Structural equation modelling indicated that the SIRDE model fit the data and largely supported four sets of hypotheses derived from the model. Specifically, (1) those with a stronger Scottish identity, (2) those who felt frustrated and angry that Scottish people are discriminated against in British society, and (3) those who believed that Scottish people are not able to improve their relatively poor social conditions within the United Kingdom (a lack of collective efficacy) were more likely to hold separatist beliefs. Further, the relationships between identity, relative deprivation, and collective efficacy, on the one hand, and voting for Scotland's independence, on the other, were fully mediated by separatist social change beliefs. Consistent with the specificity of the model, neither political engagement nor personal relative deprivation were associated with voting choice, whereas the latter was associated with lower life satisfaction. The implications and limitations of these findings are discussed. © 2017 The British Psychological Society.

Digitization of Microfilm: A Scottish Perspective.

Science.gov (United States)

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…

Minor parties and independents in times of change: Scottish local elections 1974 to 2007

OpenAIRE

Bochel, Hugh; Denver, David

2008-01-01

This article explores the electoral performance of minor party and Independent candidates in Scottish local elections from 1974 to 2007. This is a period which began with a major restructuring of local government and ended with a change in the electoral system from first-past-the-post to the single transferable vote. It encompasses a second restructuring in the 1990s, the consolidation of the Scottish National Party as an electoral force, and the creation of the Scottish Parliament. Throughou...

Epidemiology Data from the Scottish Health and Ethnicity Linkage Study (SHELS

Directory of Open Access Journals (Sweden)

Judith Fernandez

2014-11-01

Full Text Available We linked the 2001 Scottish Census, which contains ethnicity, socio-economic and demographic data to health and death records, creating an anonymised retrospective cohort study of 4.65 million people to assess the association between ethnicity and health outcomes in Scotland. The databases contain data mostly from hospital discharge and mortality records, but also from other registers.  The databases are stored in a safe haven at the National Records of Scotland (NRS. NRS is currently exploring the feasibility of making Scottish Health and Ethnicity Linkage Study (SHELS data open access while ensuring that the same level of confidentiality is maintained. If SHELS becomes open access it could be reused, with the appropriate approvals, to assess the influence of other socio-economic or demographic measures on the Scottish population’s health.

Epidemiology and outcomes of older patients admitted to Scottish intensive care units: a national database linkage study.

Science.gov (United States)

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 (Scottish Intensive Care Society, Scottish Society of Anaesthetists, Edinburgh Anaesthetics Research and Education Fund. Copyright © 2015 Elsevier Ltd. All rights reserved.

Bacterial membrane proteomics.

Science.gov (United States)

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.

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

Science.gov (United States)

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'.

Managing radioactive waste safely. Awareness and attitudes of the Scottish public

International Nuclear Information System (INIS)

Rodger, N.

2002-01-01

Between January and April 2002, the Scottish Executive Environment and Rural Affairs department inducted a consultation exercise in conjunction with DEFRA on 'Managing Radioactive Waste Safely', and commissioned several pieces of supplementary research to gauge levels of awareness of the issues around radioactive waste among the Scottish public. This research was conducted as part of this process. Its main aims were to measure awareness and assess attitudes towards radioactive waste, its sources, its perceived risks and its management. Reflecting a key objective of the main consultation, this research also sought to assess how the public rate a variety of possible actions that could be taken to involve them in this debate and decision-making process. A representative sample of 1,000 Scottish adults (age 18+) was interviewed by telephone using 'Computer Assisted Telephone Interviewing' during February 2002

Project-Based Learning in Scottish Prisons

Science.gov (United States)

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…

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Proteome scale identification, classification and structural analysis of iron-binding proteins in bread wheat.

Science.gov (United States)

Verma, Shailender Kumar; Sharma, Ankita; Sandhu, Padmani; Choudhary, Neha; Sharma, Shailaja; Acharya, Vishal; Akhter, Yusuf

2017-05-01

Bread wheat is one of the major staple foods of worldwide population and iron plays a significant role in growth and development of the plant. In this report, we are presenting the genome wide identification of iron-binding proteins in bread wheat. The wheat genome derived putative proteome was screened for identification of iron-binding sequence motifs. Out of 602 putative iron-binding proteins, 130 were able to produce reliable structural models by homology techniques and further analyzed for the presence of iron-binding structural motifs. The computationally identified proteins appear to bind to ferrous and ferric ions and showed diverse coordination geometries. Glu, His, Asp and Cys amino acid residues were found to be mostly involved in iron binding. We have classified these proteins on the basis of their localization in the different cellular compartments. The identified proteins were further classified into their protein folds, families and functional classes ranging from structure maintenance of cellular components, regulation of gene expression, post translational modification, membrane proteins, enzymes, signaling and storage proteins. This comprehensive report regarding structural iron binding proteome provides useful insights into the diversity of iron binding proteins of wheat plants and further utilized to study their roles in plant growth, development and physiology. Copyright © 2017 Elsevier Inc. All rights reserved.

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

Science.gov (United States)

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…

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

Science.gov (United States)

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.

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

Science.gov (United States)

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

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.

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.

Science.gov (United States)

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…

Jan Culik on the Scottish independence referendum

OpenAIRE

Culik, Jan

2014-01-01

A live interview with Jan Culik on the results and the political circumstances of the referendum on Scottish independence, broadcast from the BBC Pacific Quay studios. The interview was transmitted on Friday 19th September, 2014, by the nationwide Czech public service Radio (Radiozurnal) from 10 to 11 am.

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

Science.gov (United States)

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…

1001 Proteomes: a functional proteomics portal for the analysis of Arabidopsis thaliana accessions.

Science.gov (United States)

Joshi, Hiren J; Christiansen, Katy M; Fitz, Joffrey; Cao, Jun; Lipzen, Anna; Martin, Joel; Smith-Moritz, A Michelle; Pennacchio, Len A; Schackwitz, Wendy S; Weigel, Detlef; Heazlewood, Joshua L

2012-05-15

The sequencing of over a thousand natural strains of the model plant Arabidopsis thaliana is producing unparalleled information at the genetic level for plant researchers. To enable the rapid exploitation of these data for functional proteomics studies, we have created a resource for the visualization of protein information and proteomic datasets for sequenced natural strains of A. thaliana. The 1001 Proteomes portal can be used to visualize amino acid substitutions or non-synonymous single-nucleotide polymorphisms in individual proteins of A. thaliana based on the reference genome Col-0. We have used the available processed sequence information to analyze the conservation of known residues subject to protein phosphorylation among these natural strains. The substitution of amino acids in A. thaliana natural strains is heavily constrained and is likely a result of the conservation of functional attributes within proteins. At a practical level, we demonstrate that this information can be used to clarify ambiguously defined phosphorylation sites from phosphoproteomic studies. Protein sets of available natural variants are available for download to enable proteomic studies on these accessions. Together this information can be used to uncover the possible roles of specific amino acids in determining the structure and function of proteins in the model plant A. thaliana. An online portal to enable the community to exploit these data can be accessed at http://1001proteomes.masc-proteomics.org/

A gradient of mercury concentrations in Scottish single malt whiskies.

Science.gov (United States)

Rose, Neil L; Yang, Handong; Turner, Simon D

2016-02-01

Mercury (Hg) concentrations were measured in 26 Scottish single malt whiskies, and all found to be very low (mercury emissions and deposition over the last 200 years affecting concentrations in local waters used in whisky production. As UK atmospheric emissions of mercury have declined by 90 % since the 1970s, we suggest that whisky being produced today should have even lower Hg concentrations when consumed in 10- to 15-years time. This reduction may be compromised by the remobilisation of contaminants stored in catchment soils being transferred to source waters, but is very unlikely to raise the negligible health risk due to Hg from Scottish single malt whisky consumption.

Accounting for risk conflicts in Scottish salmon farming

NARCIS (Netherlands)

Georgakopoulos, G.; Thomson, I.; Kaldis, P.

2008-01-01

Purpose: To offer a theoretical analysis, inspired by contemporary research into risk, of the social and environmental accounting processes observed in an empirical study on Scottish salmon farming. Methodology / Approach: This paper used a Grounded Theory approach. Empirical evidence was collected

Proteomic approaches in research of cyanobacterial photosynthesis.

Science.gov (United States)

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.

Plant cell wall proteomics: mass spectrometry data, a trove for research on protein structure/function relationships.

Science.gov (United States)

Albenne, Cécile; Canut, Hervé; Boudart, Georges; Zhang, Yu; San Clemente, Hélène; Pont-Lezica, Rafael; Jamet, Elisabeth

2009-09-01

Proteomics allows the large-scale study of protein expression either in whole organisms or in purified organelles. In particular, mass spectrometry (MS) analysis of gel-separated proteins produces data not only for protein identification, but for protein structure, location, and processing as well. An in-depth analysis was performed on MS data from etiolated hypocotyl cell wall proteomics of Arabidopsis thaliana. These analyses show that highly homologous members of multigene families can be differentiated. Two lectins presenting 93% amino acid identity were identified using peptide mass fingerprinting. Although the identification of structural proteins such as extensins or hydroxyproline/proline-rich proteins (H/PRPs) is arduous, different types of MS spectra were exploited to identify and characterize an H/PRP. Maturation events in a couple of cell wall proteins (CWPs) were analyzed using site mapping. N-glycosylation of CWPs as well as the hydroxylation or oxidation of amino acids were also explored, adding information to improve our understanding of CWP structure/function relationships. A bioinformatic tool was developed to locate by means of MS the N-terminus of mature secreted proteins and N-glycosylation.

Proteomic analysis of human tooth pulp: proteomics of human tooth.

Science.gov (United States)

Eckhardt, Adam; Jágr, Michal; Pataridis, Statis; Mikšík, Ivan

2014-12-01

The unique pulp-dentin complex demonstrates strong regenerative potential, which enables it to respond to disease and traumatic injury. Identifying the proteins of the pulp-dentin complex is crucial to understanding the mechanisms of regeneration, tissue calcification, defense processes, and the reparation of dentin by dental pulp. The lack of knowledge of these proteins limits the development of more efficient therapies. The proteomic profile of human tooth pulp was investigated and compared with the proteome of human dentin and blood. The samples of tooth pulp were obtained from 5 sound permanent human third molars of 5 adults (n = 5). The extracted proteins were separated by 2-dimensional gel electrophoresis, analyzed by nano-liquid chromatography tandem mass spectrometry, and identified by correlating mass spectra to the proteomic databases. A total of 342 proteins were identified with high confidence, and 2 proteins were detected for the first time in an actual human sample. The identified tooth pulp proteins have a variety of functions: structural, catalytic, transporter, protease activity, immune response, and many others. In a comparison with dentin and blood plasma, 140 (pulp/dentin) shared proteins were identified, 37 of which were not observed in plasma. It can be suggested that they might participate in the unique pulp-dentin complex. This proteomic investigation of human tooth pulp, together with the previously published study of human dentin, is one of the most comprehensive proteome lists of human teeth to date. Copyright © 2014 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

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

Science.gov (United States)

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.

Predicting DNA-binding proteins and binding residues by complex structure prediction and application to human proteome.

Directory of Open Access Journals (Sweden)

Huiying Zhao

Full Text Available As more and more protein sequences are uncovered from increasingly inexpensive sequencing techniques, an urgent task is to find their functions. This work presents a highly reliable computational technique for predicting DNA-binding function at the level of protein-DNA complex structures, rather than low-resolution two-state prediction of DNA-binding as most existing techniques do. The method first predicts protein-DNA complex structure by utilizing the template-based structure prediction technique HHblits, followed by binding affinity prediction based on a knowledge-based energy function (Distance-scaled finite ideal-gas reference state for protein-DNA interactions. A leave-one-out cross validation of the method based on 179 DNA-binding and 3797 non-binding protein domains achieves a Matthews correlation coefficient (MCC of 0.77 with high precision (94% and high sensitivity (65%. We further found 51% sensitivity for 82 newly determined structures of DNA-binding proteins and 56% sensitivity for the human proteome. In addition, the method provides a reasonably accurate prediction of DNA-binding residues in proteins based on predicted DNA-binding complex structures. Its application to human proteome leads to more than 300 novel DNA-binding proteins; some of these predicted structures were validated by known structures of homologous proteins in APO forms. The method [SPOT-Seq (DNA] is available as an on-line server at http://sparks-lab.org.

Scottish Premier League Reading Stars Evaluation Report

Science.gov (United States)

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…

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Student Engagement in the Scottish Quality Enhancement Framework

Science.gov (United States)

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…

A dominant TRPV4 variant underlies osteochondrodysplasia in Scottish fold cats.

Science.gov (United States)

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.

Scottish Power Annual Report and Accounts - 1996-97

International Nuclear Information System (INIS)

1997-01-01

The annual report and accounts of Scottish Power for 1996-97 outlines the operational and financial highlights of the year, and presents the reports of the Chairman and other Directors. Details are given of the financial year, the accounting policy, profits and losses, and company and shareholder information. (UK)

Murray Pittock, ed., The Edinburgh Companion to Scottish Romanticism.

Directory of Open Access Journals (Sweden)

Manfred Malzahn

2013-10-01

Full Text Available Murray Pittock, ed., The Edinburgh Companion to Scottish Romanticism. Edinburgh: Edinburgh University Press, 2011. Pp. 251. ISBN 978-0-7486-3845-1 (hardback. £ 65.00. ISBN 978-0-7486-3846-8 (paperback. £ 21.99.

Scottish Universities Research and Reactor Centre annual report 1987-1988

International Nuclear Information System (INIS)

Whitley, J.E.

1988-01-01

The Scottish Universities Research and Reactor Centre (SURRC) provides facilities for research in isotopic, nuclear and earth sciences and collaborates with Scottish University departments on a wide range of research topics. One of its main areas of work is the Isotope Geology Unit. This has worked with the Nuclear Medicine Unit on the application of enriched stable isotope tracers in the biological and clinical sciences. The measurement of radioactive isomers is applied to quaternary geology, archaeology, nuclear medicine, health physics, oceanography, atomospheric sciences, environmental chemistry, nuclear waste disposal and mathematical modelling of the environment. There are also radiocarbon dating facilities. The facilities and the research undertaken at the Centre in the year 1987-1988, the Centre's twenty-fifth year are summarized in this report. (U.K.)

Proteomics Core

Data.gov (United States)

Federal Laboratory Consortium — Proteomics Core is the central resource for mass spectrometry based proteomics within the NHLBI. The Core staff help collaborators design proteomics experiments in a...

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

Science.gov (United States)

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.

Mass Spectrometry-Based Proteomics for the Analysis of Chromatin Structure and Dynamics

Directory of Open Access Journals (Sweden)

Monica Soldi

2013-03-01

Full Text Available Chromatin is a highly structured nucleoprotein complex made of histone proteins and DNA that controls nearly all DNA-dependent processes. Chromatin plasticity is regulated by different associated proteins, post-translational modifications on histones (hPTMs and DNA methylation, which act in a concerted manner to enforce a specific “chromatin landscape”, with a regulatory effect on gene expression. Mass Spectrometry (MS has emerged as a powerful analytical strategy to detect histone PTMs, revealing interplays between neighbouring PTMs and enabling screens for their readers in a comprehensive and quantitative fashion. Here we provide an overview of the recent achievements of state-of-the-art mass spectrometry-based proteomics for the detailed qualitative and quantitative characterization of histone post-translational modifications, histone variants, and global interactomes at specific chromatin regions. This synopsis emphasizes how the advances in high resolution MS, from “Bottom Up” to “Top Down” analysis, together with the uptake of quantitative proteomics methods by chromatin biologists, have made MS a well-established method in the epigenetics field, enabling the acquisition of original information, highly complementary to that offered by more conventional, antibody-based, assays.

Dentistry proteomics: from laboratory development to clinical practice.

Science.gov (United States)

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.

A Review of The Architecture of the Scottish Medieval Church 1100–1560

OpenAIRE

Campbell, Ian

2013-01-01

If ever a book could be described as a ‘magnum opus’ it is this: indeed it is a summa. Richard Fawcett has been publishing on Scottish medieval architecture, mainly ecclesiastical, for three decades, ranging from articles on minute changes in Gothic mouldings (the subject of his doctoral research at the University of East Anglia) such as ‘Dunblane Cathedral: evidence for a change in the design of the nave’ (1982) to a survey of architecture between 370 and 1560, Scottish Architecture from the...

The Path to Enlightenment: Making Sense of Genomic and Proteomic Information

OpenAIRE

Maurer, Martin H.

2016-01-01

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 an...

Censorship Challenges to Books in Scottish Public Libraries

Science.gov (United States)

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 deprivation and prognosis in Scottish patients with pulmonary arterial hypertension.

Science.gov (United States)

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.

Proteomics - new analytical approaches

International Nuclear Information System (INIS)

Hancock, W.S.

2001-01-01

Full text: Recent developments in the sequencing of the human genome have indicated that the number of coding gene sequences may be as few as 30,000. It is clear, however, that the complexity of the human species is dependent on the much greater diversity of the corresponding protein complement. Estimates of the diversity (discrete protein species) of the human proteome range from 200,000 to 300,000 at the lower end to 2,000,000 to 3,000,000 at the high end. In addition, proteomics (the study of the protein complement to the genome) has been subdivided into two main approaches. Global proteomics refers to a high throughput examination of the full protein set present in a cell under a given environmental condition. Focused proteomics refers to a more detailed study of a restricted set of proteins that are related to a specified biochemical pathway or subcellular structure. While many of the advances in proteomics will be based on the sequencing of the human genome, de novo characterization of protein microheterogeneity (glycosylation, phosphorylation and sulfation as well as the incorporation of lipid components) will be required in disease studies. To characterize these modifications it is necessary to digest the protein mixture with an enzyme to produce the corresponding mixture of peptides. In a process analogous to sequencing of the genome, shot-gun sequencing of the proteome is based on the characterization of the key fragments produced by such a digest. Thus, a glycopeptide and hence a specific glycosylation motif will be identified by a unique mass and then a diagnostic MS/MS spectrum. Mass spectrometry will be the preferred detector in these applications because of the unparalleled information content provided by one or more dimensions of mass measurement. In addition, highly efficient separation processes are an absolute requirement for advanced proteomic studies. For example, a combination of the orthogonal approaches, HPLC and HPCE, can be very powerful

La “struttura ecclesiastica” dello Scottish Enlightenment. Le origini dell’illuminismo scozzese fra religione naturale e teologia razionale

Directory of Open Access Journals (Sweden)

Francesco Alicino

2011-03-01

After general considerations about the process of secularization (which spread out in Europe at that time the author analyses the peculiar evolution of relationships between the Scottish Established Church and the Scottish Enlightenment, which also affected the constitutional system in this country.

Clinical proteomics

DEFF Research Database (Denmark)

Albrethsen, Jakob; Frederiksen, Hanne; Johannsen, Trine Holm

2018-01-01

Clinical proteomics aims to deliver cost-effective multiplexing of potentially hundreds of diagnostic proteins, including distinct protein isoforms. The analytical strategy known as targeted proteomics is particularly promising because it is compatible with robust mass spectrometry (MS)-platforms...... standards and calibrants. The present challenge is to examine if targeted proteomics of IGF-I can truly measure up to the routine performance that must be expected from a clinical testing platform.......Clinical proteomics aims to deliver cost-effective multiplexing of potentially hundreds of diagnostic proteins, including distinct protein isoforms. The analytical strategy known as targeted proteomics is particularly promising because it is compatible with robust mass spectrometry (MS......)-platforms already implemented in many clinical laboratories for routine quantitation of small molecules (i.e. uHPLC coupled to triple-quadrupole MS). Progress in targeted proteomics of circulating insulin-like growth factor 1 (IGF-I) have provided valuable insights about tryptic peptides, transitions, internal...

Automation, parallelism, and robotics for proteomics.

Science.gov (United States)

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.

The safety function in Scottish Nuclear

International Nuclear Information System (INIS)

McKeown, J.

1991-01-01

The Director of Safety for Scottish Nuclear Ltd, the company which has owned and operated Scotland's nuclear power generating capacity since privatization, explains how the management of safety is realized within the company, in line with the company's motto of ''Quality, Safety, Excellence''. A commitment to the highest levels of safety management in all its aspects is emphasized, from Board level down. The various measures taken to ensure these aims are realized are explained in three broad areas, radiological protection, operational nuclear safety and industrial safety. (UK)

Maillard Proteomics: Opening New Pages

Directory of Open Access Journals (Sweden)

Alena Soboleva

2017-12-01

Full Text Available 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.

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.

Science.gov (United States)

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.

SMEs and Barriers to Skill Development: A Scottish Perspective.

Science.gov (United States)

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)

Application of proteomics to ecology and population biology.

Science.gov (United States)

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.

Cost of Mastitis in Scottish Dairy Herds with Low and High Subclinical Mastitis Problems

OpenAIRE

YALÇIN, Cengiz

2000-01-01

The aim of this study was to estimate the cost of mastitis and the contribution of each cost component of mastitis to the total mastitis induced cost in herds with low and high levels of subclinical mastitis under Scottish field conditions. It was estimated that mastitis cost £140 per cow/year to the average Scottish dairy farmer in 1996. However, this figure was as low as £69 per cow/year in herds with lower levels of subclinical mastitis, and as high as £228 cow/year in herds with high s...

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

Science.gov (United States)

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

Birth of plant proteomics in India: a new horizon.

Science.gov (United States)

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.

Characterization of the porcine synovial fluid proteome and a comparison to the plasma proteome

Directory of Open Access Journals (Sweden)

Tue Bjerg Bennike

2015-12-01

In addition, we analyzed the proteome of human plasma, and compared the proteomes to the obtained porcine synovial fluid proteome. The proteome of the two body fluids were found highly similar, underlining the detected plasma derived nature of many synovial fluid components. The healthy porcine synovial fluid proteomics data, human rheumatoid arthritis synovial fluid proteomics data used in the method optimization, human plasma proteomics data, and search results, have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD000935.

ProteomicsDB.

Science.gov (United States)

Schmidt, Tobias; Samaras, Patroklos; Frejno, Martin; Gessulat, Siegfried; Barnert, Maximilian; Kienegger, Harald; Krcmar, Helmut; Schlegl, Judith; Ehrlich, Hans-Christian; Aiche, Stephan; Kuster, Bernhard; Wilhelm, Mathias

2018-01-04

ProteomicsDB (https://www.ProteomicsDB.org) is a protein-centric in-memory database for the exploration of large collections of quantitative mass spectrometry-based proteomics data. ProteomicsDB was first released in 2014 to enable the interactive exploration of the first draft of the human proteome. To date, it contains quantitative data from 78 projects totalling over 19k LC-MS/MS experiments. A standardized analysis pipeline enables comparisons between multiple datasets to facilitate the exploration of protein expression across hundreds of tissues, body fluids and cell lines. We recently extended the data model to enable the storage and integrated visualization of other quantitative omics data. This includes transcriptomics data from e.g. NCBI GEO, protein-protein interaction information from STRING, functional annotations from KEGG, drug-sensitivity/selectivity data from several public sources and reference mass spectra from the ProteomeTools project. The extended functionality transforms ProteomicsDB into a multi-purpose resource connecting quantification and meta-data for each protein. The rich user interface helps researchers to navigate all data sources in either a protein-centric or multi-protein-centric manner. Several options are available to download data manually, while our application programming interface enables accessing quantitative data systematically. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

The Scottish book mathematics from the Scottish café, with selected problems from the new Scottish book

CERN Document Server

Mauldin, R Daniel

2015-01-01

The second edition of this book updates and expands upon a historically important collection of mathematical problems first published in the United States by Birkhäuser in 1981. These problems serve as a record of the informal discussions held by a group of mathematicians at the Scottish Café in Lwów, Poland, between the two world wars. Many of them were leaders in the development of such areas as functional and real analysis, group theory, measure and set theory, probability, and topology. Finding solutions to the problems they proposed has been ongoing since World War II, with prizes offered in many cases to those who are successful. In the 35 years since the first edition published, several more problems have been fully or partially solved, but even today many still remain unsolved and several prizes remain unclaimed. In view of this, the editor has gathered new and updated commentaries on the original 193 problems. Some problems are solved for the first time in this edition. Included again in full are ...

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

Science.gov (United States)

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.

Building ProteomeTools based on a complete synthetic human proteome

Science.gov (United States)

Zolg, Daniel P.; Wilhelm, Mathias; Schnatbaum, Karsten; Zerweck, Johannes; Knaute, Tobias; Delanghe, Bernard; Bailey, Derek J.; Gessulat, Siegfried; Ehrlich, Hans-Christian; Weininger, Maximilian; Yu, Peng; Schlegl, Judith; Kramer, Karl; Schmidt, Tobias; Kusebauch, Ulrike; Deutsch, Eric W.; Aebersold, Ruedi; Moritz, Robert L.; Wenschuh, Holger; Moehring, Thomas; Aiche, Stephan; Huhmer, Andreas; Reimer, Ulf; Kuster, Bernhard

2018-01-01

The ProteomeTools project builds molecular and digital tools from the human proteome to facilitate biomedical and life science research. Here, we report the generation and multimodal LC-MS/MS analysis of >330,000 synthetic tryptic peptides representing essentially all canonical human gene products and exemplify the utility of this data. The resource will be extended to >1 million peptides and all data will be shared with the community via ProteomicsDB and proteomeXchange. PMID:28135259

Osteosarcoma inheritance in two families of Scottish deerhounds.

Science.gov (United States)

Dillberger, John E; McAtee, Sara Ann

2017-01-01

Osteosarcoma is the most common neoplastic disease in Scottish Deerhounds. For Deerhounds, a 2007 population-based study concluded that a single dominant genetic factor largely governed disease risk. For Greyhounds, Rottweilers, and Irish Wolfhounds, a 2013 genome-wide association study found multiple genetic markers in each breed, with each marker only weakly associated with the disease. We obtained from two breeders the pedigrees, age (if alive) or age at death, and osteosarcoma status for two families of Scottish Deerhounds, designated Cohorts K and T. A dog was considered unaffected only if it was osteosarcoma-free and at least 8.5 years old. We analyzed the data in two ways, by assuming either a single recessive genetic factor or a single dominant genetic factor with high penetrance. Cohort K contained 54 evaluable dogs representing 12 litters. Cohort T contained 56 evaluable dogs representing eight litters. Osteosarcoma seemed clearly heritable in both cohorts; however, having a parent with osteosarcoma raised a pup's risk of developing osteosarcoma to 38% for Cohort K but 78% for Cohort T, suggesting the possibility of different genetic risk factors in each cohort. In Cohort K, osteosarcoma inheritance fit well with a single, recessive, autosomal risk factor, although we could not rule out the possibility of a single dominant risk factor with incomplete penetrance. In Cohort T, inheritance could be explained well by a single, dominant, autosomal risk factor but was inconsistent with recessive expression. Inheritance of osteosarcoma in two Scottish Deerhound families could be explained well by a single genetic risk factor residing on an autosome, consistent with a 2007 report. In one family, inheritance was consistent with dominant expression, as previously reported. In the other family, inheritance fit better with recessive expression, although the possibility of a dominant genetic factor influenced by one or more other genetic factors could not be ruled

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

Science.gov (United States)

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.

Contemporary role of the kilt and tartan in the construction and expression of Scottish American identity

OpenAIRE

Maitland Hume, Ian M.

2001-01-01

This study explores how influential the kilt and tartan are in the way Americans perceive and express their identity in Scottish terms. Its principal focus is directed on individuals who wear the kilt in America today. The reasons which prompt people to consider qualifying their American identity are considered in the context of a number of different Scottish American organisations and community activities. These are prefaced by an appraisal of contemporary attitudes to ...

Skeletal carbonate mineralogy of Scottish bryozoans

Science.gov (United States)

Spencer Jones, Mary; Najorka, Jens; Smith, Abigail M.

2018-01-01

This paper describes the skeletal carbonate mineralogy of 156 bryozoan species collected from Scotland (sourced both from museum collections and from waters around Scotland) and collated from literature. This collection represents 79% of the species which inhabit Scottish waters and is a greater number and proportion of extant species than any previous regional study. The study is also of significance globally where the data augment the growing database of mineralogical analyses and offers first analyses for 26 genera and four families. Specimens were collated through a combination of field sampling and existing collections and were analysed by X-ray diffraction (XRD) and micro-XRD to determine wt% MgCO3 in calcite and wt% aragonite. Species distribution data and phylogenetic organisation were applied to understand distributional, taxonomic and phylo-mineralogical patterns. Analysis of the skeletal composition of Scottish bryozoans shows that the group is statistically different from neighbouring Arctic fauna but features a range of mineralogy comparable to other temperate regions. As has been previously reported, cyclostomes feature low Mg in calcite and very little aragonite, whereas cheilostomes show much more variability, including bimineralic species. Scotland is a highly variable region, open to biological and environmental influx from all directions, and bryozoans exhibit this in the wide range of within-species mineralogical variability they present. This plasticity in skeletal composition may be driven by a combination of environmentally-induced phenotypic variation, or physiological factors. A flexible response to environment, as manifested in a wide range of skeletal mineralogy within a species, may be one characteristic of successful invasive bryozoans. PMID:29897916

Barriers to Higher Education Entry--A Scottish Rural Perspective

Science.gov (United States)

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,…

Access to bank finance for Scottish SMEs.

OpenAIRE

North, David J.; Baldock, Robert; Deakins, David; Whittam, Geoff

2008-01-01

There is evidence that some SMEs may still face difficulties in accessing bank finance from lenders (CEEDR, 2007). This paper reports an in-depth study into demand and supply side issues relating to access to bank finance by Scottish SMEs and whether there is still market\\ud failure associated with good, bankable business cases from SMEs that do not receive finance. We argue that our study utilises innovative methodology and is relatively rare as a robust study in this area. We combine demand...

Clinical veterinary proteomics: Techniques and approaches to decipher the animal plasma proteome.

Science.gov (United States)

Ghodasara, P; Sadowski, P; Satake, N; Kopp, S; Mills, P C

2017-12-01

Over the last two decades, technological advancements in the field of proteomics have advanced our understanding of the complex biological systems of living organisms. Techniques based on mass spectrometry (MS) have emerged as powerful tools to contextualise existing genomic information and to create quantitative protein profiles from plasma, tissues or cell lines of various species. Proteomic approaches have been used increasingly in veterinary science to investigate biological processes responsible for growth, reproduction and pathological events. However, the adoption of proteomic approaches by veterinary investigators lags behind that of researchers in the human medical field. Furthermore, in contrast to human proteomics studies, interpretation of veterinary proteomic data is difficult due to the limited protein databases available for many animal species. This review article examines the current use of advanced proteomics techniques for evaluation of animal health and welfare and covers the current status of clinical veterinary proteomics research, including successful protein identification and data interpretation studies. It includes a description of an emerging tool, sequential window acquisition of all theoretical fragment ion mass spectra (SWATH-MS), available on selected mass spectrometry instruments. This newly developed data acquisition technique combines advantages of discovery and targeted proteomics approaches, and thus has the potential to advance the veterinary proteomics field by enhancing identification and reproducibility of proteomics data. Copyright © 2017 Elsevier Ltd. All rights reserved.

Origin and Evolution of Protein Fold Designs Inferred from Phylogenomic Analysis of CATH Domain Structures in Proteomes

Science.gov (United States)

Bukhari, Syed Abbas; Caetano-Anollés, Gustavo

2013-01-01

The spatial arrangements of secondary structures in proteins, irrespective of their connectivity, depict the overall shape and organization of protein domains. These features have been used in the CATH and SCOP classifications to hierarchically partition fold space and define the architectural make up of proteins. Here we use phylogenomic methods and a census of CATH structures in hundreds of genomes to study the origin and diversification of protein architectures (A) and their associated topologies (T) and superfamilies (H). Phylogenies that describe the evolution of domain structures and proteomes were reconstructed from the structural census and used to generate timelines of domain discovery. Phylogenies of CATH domains at T and H levels of structural abstraction and associated chronologies revealed patterns of reductive evolution, the early rise of Archaea, three epochs in the evolution of the protein world, and patterns of structural sharing between superkingdoms. Phylogenies of proteomes confirmed the early appearance of Archaea. While these findings are in agreement with previous phylogenomic studies based on the SCOP classification, phylogenies unveiled sharing patterns between Archaea and Eukarya that are recent and can explain the canonical bacterial rooting typically recovered from sequence analysis. Phylogenies of CATH domains at A level uncovered general patterns of architectural origin and diversification. The tree of A structures showed that ancient structural designs such as the 3-layer (αβα) sandwich (3.40) or the orthogonal bundle (1.10) are comparatively simpler in their makeup and are involved in basic cellular functions. In contrast, modern structural designs such as prisms, propellers, 2-solenoid, super-roll, clam, trefoil and box are not widely distributed and were probably adopted to perform specialized functions. Our timelines therefore uncover a universal tendency towards protein structural complexity that is remarkable. PMID:23555236

Anti-TNF therapy for paediatric IBD: the Scottish national experience.

Science.gov (United States)

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 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.

Clinical proteomics: Current status, challenges, and future perspectives

Directory of Open Access Journals (Sweden)

Shyh-Horng Chiou

2011-01-01

Full Text Available This account will give an overview and evaluation of the current advances in mass spectrometry (MS-based proteomics platforms and technology. A general review of some background information concerning the application of these methods in the characterization of molecular sizes and related protein expression profiles associated with different types of cells under varied experimental conditions will be presented. It is intended to provide a concise and succinct overview to those clinical researchers first exposed to this foremost powerful methodology in modern life sciences of postgenomic era. Proteomic characterization using highly sophisticated and expensive instrumentation of MS has been used to characterize biological samples of complex protein mixtures with vastly different protein structure and composition. These systems are then used to highlight the versatility and potential of the MS-based proteomic strategies for facilitating protein expression analysis of various disease-related organisms or tissues of interest. Major MS-based strategies reviewed herein include (1 matrix-assisted laser desorption ionization-MS and electron-spray ionization proteomics; (2 one-dimensional or two-dimensional gel-based proteomics; (3 gel-free shotgun proteomics in conjunction with liquid chromatography/tandem MS; (4 Multiple reaction monitoring coupled tandem MS quantitative proteomics and; (5 Phosphoproteomics based on immobilized metal affinity chromatography and liquid chromatography-MS/MS.

From Proteomics to Structural Studies of Cytosolic/Mitochondrial-Type Thioredoxin Systems in Barley Seeds

DEFF Research Database (Denmark)

Shahpiri, Azar; Svensson, Birte; Finnie, Christine

2009-01-01

Thioredoxins (Trx) are ubiquitous proteins that participate in thiol disulfide reactions via two active site cysteine residues, allowing Trx to reduce disulfide bonds in target proteins. Recent progress in proteome analysis has resulted in identification of a wide range of potential target proteins...... for Trx, indicating that Trx plays a key role in several aspects of cell metabolism. In contrast to other organisms, plants contain multiple forms of Trx that are classified based on their primary structures and sub-cellular localization. The reduction of cytosolic and mitochondrial types of Trx...

A perspective on extracellular vesicles proteomics

Science.gov (United States)

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.

C4 photosynthetic machinery: insights from maize chloroplast proteomics

Directory of Open Access Journals (Sweden)

Qi eZhao

2013-04-01

Full Text Available C4 plants exhibit much higher CO2 assimilation rates than C3 plants. The specialized differentiation of mesophyll cell (M and bundle sheath cell (BS type chloroplasts is unique to C4 plants and improves photosynthesis efficiency. Maize (Zea mays is an important crop and model with C4 photosynthetic machinery. Current high-throughput quantitative proteomics approaches (e.g., 2DE, iTRAQ, and shotgun proteomics have been employed to investigate maize chloroplast structure and function. These proteomic studies have provided valuable information on C4 chloroplast protein components, photosynthesis, and other metabolic mechanisms underlying chloroplast biogenesis, stromal and membrane differentiation, as well as response to salinity, high/low temperature, and light stress. This review presents an overview of proteomics advances in maize chloroplast biology.

Barley seed proteomics from spots to structures

DEFF Research Database (Denmark)

Finnie, Christine; Svensson, Birte

2009-01-01

forms on 2D-gels. Specific protein families, including peroxidases and alpha-amylases have been subjected to in-depth analysis resulting in characterisation of different isozymes, post-translational. modifications and processing. A functional proteomics study focusing on the seed thioredoxin system has...... with information from rice and other cereals facilitate identification of barley proteins. Several hundred barley seed proteins are identified and lower abundance proteins including membrane proteins are now being analysed. In the present review we focus on variation in protein profiles of seed tissues during...

Proteomics dataset

DEFF Research Database (Denmark)

Bennike, Tue Bjerg; Carlsen, Thomas Gelsing; Ellingsen, Torkell

2017-01-01

The datasets presented in this article are related to the research articles entitled “Neutrophil Extracellular Traps in Ulcerative Colitis: A Proteome Analysis of Intestinal Biopsies” (Bennike et al., 2015 [1]), and “Proteome Analysis of Rheumatoid Arthritis Gut Mucosa” (Bennike et al., 2017 [2])...... been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD001608 for ulcerative colitis and control samples, and PXD003082 for rheumatoid arthritis samples....

Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation

Science.gov (United States)

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

Anna Groundwater, The Scottish Middle March 1573-1625: Power, Kinship, Allegiance

Directory of Open Access Journals (Sweden)

Janine van Vliet

2011-09-01

Full Text Available Anna Groundwater. The Scottish Middle March 1573-1625: Power, Kinship, Allegiance. Royal Historical Society Studies in History, New Series. Woodbridge, UK: The Boydell Press, 2010. Pp. 236. ISBN 978-0-86193-307-5. £50.00; US$90.00.

The Presbyterian Churches in New South Wales, 1823-1865 : with particular reference to their Scottish relations

OpenAIRE

Bridges, Barry John

1987-01-01

This study covers the period from arrival of the first minister to union of most congregations in a Church unconnected with the Scottish parent Churches. My thesis is that reliance on the Scottish Churches was a necessary condition for establishment of the Presbyterian Church in the Colony but also the principal cause of failure to attempt to become a major religious force. Equality with the Church of England was conceded gradually and, initially, reluctantly and from the first State aid and ...

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

Science.gov (United States)

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.

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

Science.gov (United States)

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)

Developing and Rewarding Excellent Teachers: The Scottish Chartered Teacher Scheme

Science.gov (United States)

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…

Proteomics research in India: an update.

Science.gov (United States)

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.

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

Science.gov (United States)

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…

The core proteome and pan proteome of Salmonella Paratyphi A epidemic strains.

Directory of Open Access Journals (Sweden)

Li Zhang

Full Text Available Comparative proteomics of the multiple strains within the same species can reveal the genetic variation and relationships among strains without the need to assess the genomic data. Similar to comparative genomics, core proteome and pan proteome can also be obtained within multiple strains under the same culture conditions. In this study we present the core proteome and pan proteome of four epidemic Salmonella Paratyphi A strains cultured under laboratory culture conditions. The proteomic information was obtained using a Two-dimensional gel electrophoresis (2-DE technique. The expression profiles of these strains were conservative, similar to the monomorphic genome of S. Paratyphi A. Few strain-specific proteins were found in these strains. Interestingly, non-core proteins were found in similar categories as core proteins. However, significant fluctuations in the abundance of some core proteins were also observed, suggesting that there is elaborate regulation of core proteins in the different strains even when they are cultured in the same environment. Therefore, core proteome and pan proteome analysis of the multiple strains can demonstrate the core pathways of metabolism of the species under specific culture conditions, and further the specific responses and adaptations of the strains to the growth environment.

Quantitative, high-resolution proteomics for data-driven systems biology

DEFF Research Database (Denmark)

Cox, J.; Mann, M.

2011-01-01

Systems biology requires comprehensive data at all molecular levels. Mass spectrometry (MS)-based proteomics has emerged as a powerful and universal method for the global measurement of proteins. In the most widespread format, it uses liquid chromatography (LC) coupled to high-resolution tandem...... primary structure of proteins including posttranslational modifications, to localize proteins to organelles, and to determine protein interactions. Here, we describe the principles of analysis and the areas of biology where proteomics can make unique contributions. The large-scale nature of proteomics...... data and its high accuracy pose special opportunities as well as challenges in systems biology that have been largely untapped so far....

Resolution of lameness associated with Scottish fold osteodystrophy following bilateral ostectomies and pantarsal arthrodeses: a case report

International Nuclear Information System (INIS)

Mathews, K.G.; Koblik, P.D.; Knoeckel, M.J.; Pool, R.R.; Fyfe, J.C.

1995-01-01

Bilateral hind-limb lameness, associated with tarsal exostoses in a Scottish fold diagnosed as having Scottish fold osteodystrophy, resolved following staged bilateral ostectomies and pantarsal arthrodeses. Degenerative changes in the phalangeal joints of the hind limbs have progressed radiographically, but lameness has not recurred 48 weeks following the second arthrodesis. Additional skeletal abnormalities were detected radiographically in both carpi and in several caudal vertebrae. A partial, left-sided conduction deafness was diagnosed by evaluating brain stem auditory-evoked responses

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

Science.gov (United States)

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.

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

Science.gov (United States)

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

A Comparison of Science Word Meaning in the Classrooms of Two Different Countries: Scottish Integrated Science in Scotland and in Malaysia.

Science.gov (United States)

Isa, A. M.; Maskill, R.

1982-01-01

Investigates the difference between two groups of adolescents learning basic science from the same curriculum (Scottish Integrated Science) but in two different languages and cultural settings. Word association tests distinguished between the groups, with the Malay children producing more associations than the Scottish children. (Author/JJD)

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

Science.gov (United States)

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.

A Proposal of the Ur-proteome

Science.gov (United States)

Palacios-Pérez, Miryam; Andrade-Díaz, Fernando; José, Marco V.

2017-11-01

Herein we outline a plausible proteome, encoded by assuming a primeval RNY genetic code. We unveil the primeval phenotype by using only the RNA genotype; it means that we recovered the most ancestral proteome, mostly made of the 8 amino acids encoded by RNY triplets. By looking at those fragments, it is noticeable that they are positioned, not at catalytic sites, but in the cofactor binding sites. It implies that the stabilization of a molecule appeared long before its catalytic activity, and therefore the Ur-proteome comprised a set of proteins modules that corresponded to Cofactor Stabilizing Binding Sites (CSBSs), which we call the primitive bindome. With our method, we reconstructed the structures of the "first protein modules" that Sobolevsky and Trifonov (2006) found by using only RMSD. We also examine the probable cofactors that bound to them. We discuss the notion of CSBSs as the first proteins modules in progenotes in the context of several proposals about the primitive forms of life.

Spermatogenesis in mammals: proteomic insights.

Science.gov (United States)

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

[Proteomics and transfusion medicine].

Science.gov (United States)

Lion, N; Prudent, M; Crettaz, D; Tissot, J-D

2011-04-01

The term "proteomics" covers tools and techniques that are used to analyze and characterize complex mixtures of proteins from various biological samples. In this short review, a typical proteomic approach, related to the study of particular and illustrative situation related to transfusion medicine is reported. This "case report" will allow the reader to be familiar with a practical proteomic approach of a real situation, and will permit to describe the tools that are usually used in proteomic labs, and, in a second part, to present various proteomic applications in transfusion medicine. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

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

Science.gov (United States)

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.

Dissecting plasmodesmata molecular composition by mass spectrometry-based proteomics.

Directory of Open Access Journals (Sweden)

Emmanuelle Maria Françoise Bayer

2013-01-01

Full Text Available 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 specialised domains of the endoplasmic reticulum and the plasma membrane. 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, immunolocalisation or screening of random cDNAs, only few PD proteins had been conclusively identified and characterised. 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.

Dissecting plasmodesmata molecular composition by mass spectrometry-based proteomics.

Science.gov (United States)

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.

A Review of The Architecture of the Scottish Medieval Church 1100–1560

Directory of Open Access Journals (Sweden)

Ian Campbell

2013-01-01

Full Text Available If ever a book could be described as a ‘magnum opus’ it is this: indeed it is a summa. Richard Fawcett has been publishing on Scottish medieval architecture, mainly ecclesiastical, for three decades, ranging from articles on minute changes in Gothic mouldings (the subject of his doctoral research at the University of East Anglia such as ‘Dunblane Cathedral: evidence for a change in the design of the nave’ (1982 to a survey of architecture between 370 and 1560, Scottish Architecture from the Accession of the Stewarts to the Reformation (1994. For much of that time he was an Inspector of Ancient Monuments for Historic Scotland, allowing him unfettered access to all the key monuments for most of which he has written authoritative guidebooks. However, besides Scotland, his knowledge of other European medieval architecture, especially in England, France and the Low Countries is encyclopaedic. His researches have made unsustainable the inferiorist attitude that Scottish medieval architecture was insular and backward, by pointing out countless foreign parallels, which demonstrate that Scotland’s patrons and masons were always aware of contemporary developments beyond its borders and shores. This monumental book brings together the fruits of these years of study into a rich synthesis. At last MacGibbon and Ross’ groundbreaking Ecclesiastical architecture of Scotland (1896-7 has been superseded.

Multi-Probe Investigation of Proteomic Structure of Pathogens

International Nuclear Information System (INIS)

Malkin, A J; Plomp, M; Leighton, T J; Vogelstein, B; Wheeler, K E

2008-01-01

Complete genome sequences are available for understanding biotransformation, environmental resistance and pathogenesis of microbial, cellular and pathogen systems. The present technological and scientific challenges are to unravel the relationships between the organization and function of protein complexes at cell, microbial and pathogens surfaces, to understand how these complexes evolve during the bacterial, cellular and pathogen life cycles, and how they respond to environmental changes, chemical stimulants and therapeutics. In particular, elucidating the molecular structure and architecture of human pathogen surfaces is essential to understanding mechanisms of pathogenesis, immune response, physicochemical interactions, environmental resistance and development of countermeasures against bioterrorist agents. The objective of this project was to investigate the architecture, proteomic structure, and function of bacterial spores through a combination of high-resolution in vitro atomic force microscopy (AFM) and AFM-based immunolabeling with threat-specific antibodies. Particular attention in this project was focused on spore forming Bacillus species including the Sterne vaccine strain of Bacillus anthracis and the spore forming near-neighbor of Clostridium botulinum, C. novyi-NT. Bacillus species, including B. anthracis, the causative agent of inhalation anthrax are laboratory models for elucidating spore structure/function. Even though the complete genome sequence is available for B. subtilis, cereus, anthracis and other species, the determination and composition of spore structure/function is not understood. Prof. B. Vogelstein and colleagues at the John Hopkins University have recently developed a breakthrough bacteriolytic therapy for cancer treatment (1). They discovered that intravenously injected Clostridium novyi-NT spores germinate exclusively within the avascular regions of tumors in mice and destroy advanced cancerous lesions. The bacteria were also

Predicting Use and Maintenance of Use of Substances in Scottish Adolescents.

Science.gov (United States)

Karatzias, A.; Power, K. G.; Swanson, V.

2001-01-01

Studied the roles of demographic, school, nonschool, and personality factors in predicting the use of tobacco, alcohol, and illicit drugs and maintenance of this use. Findings for 425 Scottish secondary school students show different predictive factors. Discusses implications of the findings for decreasing the prevalence of substance use. (SLD)

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Sports related injuries in Scottish adolescents aged 11-15

OpenAIRE

Williams, J. M.; Wright, P.; Currie, C. E.; Beattie, T. F.

1998-01-01

OBJECTIVES: To measure the age and sex distribution of self reported sports and leisure injuries in a 12 month retrospective recall period among a representative national sample of Scottish adolescents, and to examine the characteristics (gender, age, handedness, and level of sports participation) of sports related injuries in relation to injuries sustained during other activities. DESIGN/SETTING: Self completion questionnaire survey administered in schools during April- June 1994. SUBJ...

Principles of proteome allocation are revealed using proteomic data and genome-scale models

DEFF Research Database (Denmark)

Yang, Laurence; Yurkovich, James T.; Lloyd, Colton J.

2016-01-01

to metabolism and fitness. Using proteomics data, we formulated allocation constraints for key proteome sectors in the ME model. The resulting calibrated model effectively computed the "generalist" (wild-type) E. coli proteome and phenotype across diverse growth environments. Across 15 growth conditions......Integrating omics data to refine or make context-specific models is an active field of constraint-based modeling. Proteomics now cover over 95% of the Escherichia coli proteome by mass. Genome-scale models of Metabolism and macromolecular Expression (ME) compute proteome allocation linked...... of these sectors for the general stress response sigma factor sigma(S). Finally, the sector constraints represent a general formalism for integrating omics data from any experimental condition into constraint-based ME models. The constraints can be fine-grained (individual proteins) or coarse-grained (functionally...

Scottish independence and the all-affected interests principle

OpenAIRE

Saunders, Ben

2012-01-01

It is frequently argued that non-Scottish UK citizens should be enfranchised in any referendum on the future of Scotland because they are affected by the decision. This article argues that this position cannot in fact be supported by the all-affected interests principle for two reasons. First, a consistent application of the all-affected interests principle would require enfranchising not only all UK citizens but also many non-UK citizens who are also affected. Second, doubt is cast upon the ...

Complete fold annotation of the human proteome using a novel structural feature space.

Science.gov (United States)

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.

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

Science.gov (United States)

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.

In silico proteome analysis to facilitate proteomics experiments using mass spectrometry

Directory of Open Access Journals (Sweden)

Lindo Micheal

2003-08-01

Full Text Available Abstract Proteomics experiments typically involve protein or peptide separation steps coupled to the identification of many hundreds to thousands of peptides by mass spectrometry. Development of methodology and instrumentation in this field is proceeding rapidly, and effective software is needed to link the different stages of proteomic analysis. We have developed an application, proteogest, written in Perl that generates descriptive and statistical analyses of the biophysical properties of multiple (e.g. thousands protein sequences submitted by the user, for instance protein sequences inferred from the complete genome sequence of a model organism. The application also carries out in silico proteolytic digestion of the submitted proteomes, or subsets thereof, and the distribution of biophysical properties of the resulting peptides is presented. proteogest is customizable, the user being able to select many options, for instance the cleavage pattern of the digestion treatment or the presence of modifications to specific amino acid residues. We show how proteogest can be used to compare the proteomes and digested proteome products of model organisms, to examine the added complexity generated by modification of residues, and to facilitate the design of proteomics experiments for optimal representation of component proteins.

Genetic determinants of hair and eye colours in the Scottish and Danish populations

DEFF Research Database (Denmark)

Mengel-From, Jonas; Wong, Terence H; Morling, Niels

2009-01-01

BACKGROUND: Eye and hair colour is highly variable in the European population, and is largely genetically determined. Both linkage and association studies have previously been used to identify candidate genes underlying this variation. Many of the genes found were previously known as underlying...... mutant mouse phenotypes or human genetic disease, but others, previously unsuspected as pigmentation genes, have also been discovered. RESULTS: We assayed the hair of a population of individuals of Scottish origin using tristimulus colorimetry, in order to produce a quantitative measure of hair colour....... Cluster analysis of this data defined two groups, with overlapping borders, which corresponded to visually assessed dark versus red/light hair colour. The Danish population was assigned into categorical hair colour groups. Both cohorts were also assessed for eye colour. DNA from the Scottish group...

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

Science.gov (United States)

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…

Making proteomics data accessible and reusable: current state of proteomics databases and repositories.

Science.gov (United States)

Perez-Riverol, Yasset; Alpi, Emanuele; Wang, Rui; Hermjakob, Henning; Vizcaíno, Juan Antonio

2015-03-01

Compared to other data-intensive disciplines such as genomics, public deposition and storage of MS-based proteomics, data are still less developed due to, among other reasons, the inherent complexity of the data and the variety of data types and experimental workflows. In order to address this need, several public repositories for MS proteomics experiments have been developed, each with different purposes in mind. The most established resources are the Global Proteome Machine Database (GPMDB), PeptideAtlas, and the PRIDE database. Additionally, there are other useful (in many cases recently developed) resources such as ProteomicsDB, Mass Spectrometry Interactive Virtual Environment (MassIVE), Chorus, MaxQB, PeptideAtlas SRM Experiment Library (PASSEL), Model Organism Protein Expression Database (MOPED), and the Human Proteinpedia. In addition, the ProteomeXchange consortium has been recently developed to enable better integration of public repositories and the coordinated sharing of proteomics information, maximizing its benefit to the scientific community. Here, we will review each of the major proteomics resources independently and some tools that enable the integration, mining and reuse of the data. We will also discuss some of the major challenges and current pitfalls in the integration and sharing of the data. © 2014 The Authors. PROTEOMICS published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

hpvPDB: An Online Proteome Reserve for Human Papillomavirus

Directory of Open Access Journals (Sweden)

Satish Kumar

2013-12-01

Full Text Available Human papillomavirus (HPV infection is the leading cause of cancer mortality among women worldwide. The molecular understanding of HPV proteins has significant connotation for understanding their intrusion in the host and designing novel protein vaccines and anti-viral agents, etc. Genomic, proteomic, structural, and disease-related information on HPV is available on the web; yet, with trivial annotations and more so, it is not well customized for data analysis, host-pathogen interaction, strain-disease association, drug designing, and sequence analysis, etc. We attempted to design an online reserve with comprehensive information on HPV for the end users desiring the same. The Human Papillomavirus Proteome Database (hpvPDB domiciles proteomic and genomic information on 150 HPV strains sequenced to date. Simultaneous easy expandability and retrieval of the strain-specific data, with a provision for sequence analysis and exploration potential of predicted structures, and easy access for curation and annotation through a range of search options at one platform are a few of its important features. Affluent information in this reserve could be of help for researchers involved in structural virology, cancer research, drug discovery, and vaccine design.

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Prevalence of periradicular periodontitis in a Scottish subpopulation found on CBCT images.

Science.gov (United States)

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 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.

When proteomics reveals unsuspected roles: the plastoglobule example

Directory of Open Access Journals (Sweden)

Claire eBréhélin

2013-04-01

Full Text Available Plastoglobules are globular compartments found in plastids. Before initial proteomic studies were published, these particles were often viewed as passive lipid droplets whose unique role was to store lipids coming from the thylakoid turn-over, or to accumulate carotenoids in the chromoplasts. Yet, two proteomic studies, published concomitantly, suggested for the first time that plastoglobules are more than "junk cupboards" for lipids. Indeed, both studies demonstrated that plastoglobules do not only include structural proteins belonging to the plastoglobulin / fibrillin family, but also contain active enzymes. The specific plastoglobule localization of these enzymes has been confirmed by different approaches such as immunogold localization and GFP protein fusions, thus providing evidence that plastoglobules actively participate in diverse pathways of plastid metabolism. These proteomic studies have been the basis for numerous recent works investigating plastoglobule function. However, a lot still needs to be discovered about the molecular composition and the role of plastoglobules. In this chapter, we will describe how the proteomic approaches have launched new perspectives on plastoglobule functions.

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

Science.gov (United States)

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…

Proteomics in medical microbiology.

Science.gov (United States)

Cash, P

2000-04-01

The techniques of proteomics (high resolution two-dimensional electrophoresis and protein characterisation) are widely used for microbiological research to analyse global protein synthesis as an indicator of gene expression. The rapid progress in microbial proteomics has been achieved through the wide availability of whole genome sequences for a number of bacterial groups. Beyond providing a basic understanding of microbial gene expression, proteomics has also played a role in medical areas of microbiology. Progress has been made in the use of the techniques for investigating the epidemiology and taxonomy of human microbial pathogens, the identification of novel pathogenic mechanisms and the analysis of drug resistance. In each of these areas, proteomics has provided new insights that complement genomic-based investigations. This review describes the current progress in these research fields and highlights some of the technical challenges existing for the application of proteomics in medical microbiology. The latter concern the analysis of genetically heterogeneous bacterial populations and the integration of the proteomic and genomic data for these bacteria. The characterisation of the proteomes of bacterial pathogens growing in their natural hosts remains a future challenge.

Scottish Academy of Fashion Showcase Exhibition at Inspace Edinburgh

OpenAIRE

Gillan, Robert

2011-01-01

The Scottish Academy of Fashion (SAF) is an ambitious project to establish Scotland as a global centre for excellence in fashion related learning and commercially relevant research.Scotland has world-class education and globally recognised leaders in the fashion industry. It has a niche fashion and textile industry embedded in luxury fashion worldwide. Scotland attracts international talent to fashion-related education.SAF aims to develop an effective platform to combine these strengths, and ...

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

Science.gov (United States)

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.

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

Directory of Open Access Journals (Sweden)

Helsens Kenny

2011-03-01

Full Text Available Abstract Background 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. Results 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. Conclusions 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.

The measurement and regulation of cross subsidy. The case of the Scottish water industry

International Nuclear Information System (INIS)

Sawkins, John W.; Reid, Scott

2007-01-01

There is a widespread belief that significant cross subsidies exist in the water, gas and electricity utility industries, particularly those under public ownership. In this paper we discuss the measurement of cross subsidy and its regulatory implications in the context of a publicly owned utility on the verge of being opened up to product market competition. Using the case of the publicly owned Scottish water industry the paper outlines the definition and measurement of cross subsidy in theoretical terms before reviewing the policy debate over the desirability of cross subsidy between different customer groups and services. It then explains the approach to measurement recently adopted by the Scottish Executive. Having established the size and direction of cross subsidy the regulatory implications are considered. (author)

Income, Wealth and Health Inequalities - A Scottish Social Justice Perspective.

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Incorporating Scottish Highland Games and Activities into Your Physical Education Classes

Science.gov (United States)

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…

Data from proteomic characterization and comparison of mammalian milk fat globule proteomes by iTRAQ analysis

Directory of Open Access Journals (Sweden)

Yongxin Yang

2015-06-01

Full Text Available Milk fat globules memebrane (MFGM-enriched proteomes from Holstein, Jersey, yak, buffalo, goat, camel, horse, and human were extracted and identified by an iTRAQ quantification proteomic approach. Proteomes data were analyzed by bioinformatic and multivariate statistical analysis and used to present the characteristic traits of the MFGM proteins among the studied mammals. The data of this study are also related to the research article “Proteomic characterization and comparison of mammalian milk fat globule proteomes by iTRAQ analysis” in the Journal of Proteomics [1].

Anna Groundwater, The Scottish Middle March 1573-1625: Power, Kinship, Allegiance

OpenAIRE

Janine van Vliet

2011-01-01

Anna Groundwater. The Scottish Middle March 1573-1625: Power, Kinship, Allegiance. Royal Historical Society Studies in History, New Series. Woodbridge, UK: The Boydell Press, 2010. Pp. 236. ISBN 978-0-86193-307-5. £50.00; US$90.00.

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Progress with Scottish Nuclear Limited's dry fuel store proposals

International Nuclear Information System (INIS)

Cathro, I.S.

1994-01-01

At present Scottish Nuclear plc's largest operating cost, associated with the Advanced Gas Cooled Reactors that it manages, is the reprocessing of spent fuels. Looking to reduce the costs, the company has considered alternative disposal options. Dry vault storage has emerged as a clear leader. An adaption of the United States Modular Vault Dry Storage design is being studied in order to examine the feasibility of a store of this type at each of its power stations. (UK)

Skeletal muscle proteomic signature and metabolic impairment in pulmonary hypertension.

Science.gov (United States)

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 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.

Proteomics reveals the effects of sustained weight loss on the human plasma proteome

DEFF Research Database (Denmark)

Geyer, Philipp E; Wewer Albrechtsen, Nicolai J; Tyanova, Stefka

2016-01-01

Sustained weight loss is a preferred intervention in a wide range of metabolic conditions, but the effects on an individual's health state remain ill-defined. Here, we investigate the plasma proteomes of a cohort of 43 obese individuals that had undergone 8 weeks of 12% body weight loss followed...... by a year of weight maintenance. Using mass spectrometry-based plasma proteome profiling, we measured 1,294 plasma proteomes. Longitudinal monitoring of the cohort revealed individual-specific protein levels with wide-ranging effects of losing weight on the plasma proteome reflected in 93 significantly...

Translational plant proteomics: a perspective.

Science.gov (United States)

Agrawal, Ganesh Kumar; Pedreschi, Romina; Barkla, Bronwyn J; Bindschedler, Laurence Veronique; Cramer, Rainer; Sarkar, Abhijit; Renaut, Jenny; Job, Dominique; Rakwal, Randeep

2012-08-03

Translational proteomics is an emerging sub-discipline of the proteomics field in the biological sciences. Translational plant proteomics aims to integrate knowledge from basic sciences to translate it into field applications to solve issues related but not limited to the recreational and economic values of plants, food security and safety, and energy sustainability. In this review, we highlight the substantial progress reached in plant proteomics during the past decade which has paved the way for translational plant proteomics. Increasing proteomics knowledge in plants is not limited to model and non-model plants, proteogenomics, crop improvement, and food analysis, safety, and nutrition but to many more potential applications. Given the wealth of information generated and to some extent applied, there is the need for more efficient and broader channels to freely disseminate the information to the scientific community. This article is part of a Special Issue entitled: Translational Proteomics. Copyright © 2012 Elsevier B.V. All rights reserved.

Electricity privatisation and the Scottish coal industry

Energy Technology Data Exchange (ETDEWEB)

Davies, P.

1988-09-01

In the run up to the privatisation of the electricity supply industry in Scotland, the South of Scotland Electricity Board (SSEB) is involved in a battle for power with British Coal's Scottish area over the price of its coal, the bulk of which has been purchased by the SSEB in recent years. The SSEB has been trying to persuade British Coal to bring its prices down to those currently available on the world market. This would require a reduction of some 30%. The SSEB has backed up its requests by threatening to import more foreign coal if British Coal refuses to comply.

Proteomics in Argentina - limitations and future perspectives: A special emphasis on meat proteomics.

Science.gov (United States)

Fadda, Silvina; Almeida, André M

2015-11-01

Argentina is one of the most relevant countries in Latin America, playing a major role in regional economics, culture and science. Over the last 80 years, Argentinean history has been characterized by several upward and downward phases that had major consequences on the development of science in the country and most recently on proteomics. In this article, we characterize the evolution of Proteomics sciences in Argentina over the last decade and a half. We describe the proteomics publication output of the country in the framework of the regional and international contexts, demonstrating that Argentina is solidly anchored in a regional context, showing results similar to other emergent and Latin American countries, albeit still far from the European, American or Australian realities. We also provide a case-study on the importance of Proteomics to a specific sector in the area of food science: the use of bacteria of technological interest, highlighting major achievements obtained by Argentinean proteomics scientists. Finally, we provide a general picture of the endeavors being undertaken by Argentinean Proteomics scientists and their international collaborators to promote the Proteomics-based research with the new generation of scientists and PhD students in both Argentina and other countries in the Southern cone. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

87Sr/86Sr isotope fingerprinting of Scottish and Icelandic migratory shorebirds

International Nuclear Information System (INIS)

Evans, Jane; Bullman, Rhys

2009-01-01

Biosphere Sr isotope composition data from Iceland and Scotland suggest that terrestrially feeding birds from these two countries will have significantly different 87 Sr/ 86 Sr isotope composition in their tissues. The aim of this study is to test if these differences can be measured within the bone and feather of migratory wading birds, who feed terrestrially as juveniles, thus providing a provenance tool for these birds. The study shows that birds can be distinguished on the basis of the Sr isotope composition of their bone. The field for Icelandic birds is defined by data from juvenile common redshank (Tringa totanus) and whimbrel (Numenius phaeopus) which give 0.7056 ± 0.0012, (2σ, n = 7). The majority of Scottish birds in this study are from coastal regions and have a signature close to that of seawater of 0.7095 ± 0.0006 (2σ, n = 9). The Sr ratios in the body tissue of these two populations of all Icelandic and Scottish adult and juvenile birds analysed are significantly different (p 87 Sr/ 86 Sr values as high as 0.7194 which reflect their non-marine diet. Icelandic redshank (Tringa totanus robusta) that have flown to Scotland and returned to Iceland show the effect of the Scottish contribution to their diet with elevated values of 0.7086 ± 0.0004, (2σ, n = 6). Redshank found in Scotland that cannot be classified on the basis biometric analysis are shown to be of Icelandic origin and analysis of the primary feathers from two birds demonstrates that isotope variation between feathers could be used to track changes in diet related to the timing of individual feather growth.

Scottish hydrocarbons: Borders and bounty

International Nuclear Information System (INIS)

Roberts, John

1999-01-01

On 6 May, the people of Scotland will vote for the country's first parliament in almost three centuries. One issue is expected to arouse particularly strong views: the question of North Sea oil and gas, and who benefits from its production and taxation. Most of these hydrocarbons lie in the northern half of the British Isles, but drawing boundaries to settle contentious issues such as oil and gas fields is not an easy task. And, if boundaries were to be drawn, then a scarcely less contentious subject arises: just how much cash might an independent Scotland expect to receive? Reading between the lines it's clear that in hard cash terms, were Scotland to be independent whilst still retaining the vast bulk of North Sea oilfields, depressed prices would ensure that hydrocarbon tax revenues would be unlikely to constitute a particularly impressive addition to the Scottish Treasury. (UK)

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

Science.gov (United States)

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)

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

Science.gov (United States)

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…

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

Science.gov (United States)

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.

Scottish solar enthusiasts out and about in the North

Energy Technology Data Exchange (ETDEWEB)

Porteous, Colin (Mackintosh School of Architecture, Glasgow (United Kingdom))

1993-12-01

Each year the Scottish Solar Energy Group organises a 3-4 day visit to solar buildings or installations which are a bit further afield than Scotland's ''central belt''. This year they visited a new house overlooking Loch Ness. The Lionacleit community school in Benbecula, while of a much larger scale at abut 6000m[sup 2], is analogous to the house in that energy consciousness is addressed through a range of both active and passive measures. (author)

Proteomic Investigations into Hemodialysis Therapy

Directory of Open Access Journals (Sweden)

Mario Bonomini

2015-12-01

Full Text Available 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(incompatibility. 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.

Proteomic Investigations into Hemodialysis Therapy

Science.gov (United States)

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

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

Science.gov (United States)

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.

Organisation of the disposal of radioactive sources from Scottish hospitals

International Nuclear Information System (INIS)

Corrigall, R S; Martin, C J; Watson, I

2004-01-01

An amnesty for disposal of sealed radioactive sources from Scottish hospitals has been funded by the Scottish Executive to address problems arising from accumulation of sources. The contract was awarded to a company involved in radioactive source recycling. Coordination of uplifts from several hospitals allowed considerable financial savings to be made, so source amnesties could offer monetary advantages to Health and Education Departments elsewhere in the UK, as well as alleviating the problem from security and storage of sources that are no longer required. The sources originated in 14 hospitals, but were uplifted from five pick-up points. There were a total of 246 sources with 167 of these being caesium-137. The total activity was 16.2 TBq with one large 16.1 TBq blood irradiator source and the activities of all the other sources adding up to 167 GBq. This paper describes organisation of the collection. Options for achieving compliance with the Radioactive Substances Act 1993 are discussed, although in the event, special authorisations were obtained for each hospital. Arrangements for transport of the sources and source security were drawn up including emergency procedures for dealing with foreseeable incidents. The police provided secure overnight storage for the loaded truck and assistance in directing and monitoring progress of the load

Translational plant proteomics: A perspective

NARCIS (Netherlands)

Agrawal, G.K.; Pedreschi, R.; Barkla, B.J.; Bindschedler, L.V.; Cramer, R.; Sarkar, A.; Renaut, J.; Job, D.; Rakwal, R.

2012-01-01

Translational proteomics is an emerging sub-discipline of the proteomics field in the biological sciences. Translational plant proteomics aims to integrate knowledge from basic sciences to translate it into field applications to solve issues related but not limited to the recreational and economic

Evolution of Clinical Proteomics and its Role in Medicine | Office of Cancer Clinical Proteomics Research

Science.gov (United States)

NCI's Office of Cancer Clinical Proteomics Research authored a review of the current state of clinical proteomics in the peer-reviewed Journal of Proteome Research. The review highlights outcomes from the CPTC program and also provides a thorough overview of the different technologies that have pushed the field forward. Additionally, the review provides a vision for moving the field forward through linking advances in genomic and proteomic analysis to develop new, molecularly targeted interventions.

Income, Wealth and Health Inequalities — A Scottish Social Justice Perspective

Directory of Open Access Journals (Sweden)

Elspeth Molony

2016-04-01

Full Text Available 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.

Income, Wealth and Health Inequalities — A Scottish Social Justice Perspective

Science.gov (United States)

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

Radioactivity in Scottish soils and grassy vegetation

International Nuclear Information System (INIS)

Miller, G.R.; Horrill, A.D.; Thomson, A.J.; Howson, G.

1989-05-01

In June 1987, soil and graminoid vegetation samples were collected from 159 randomly selected Scottish sites and analysed for radioactivity due to potassium-40, caesium-134 and caesium-137. Activity due to plutonium-238 and plutonium-239/240 was also measured in soils from 47 of the sites. The main aims of this survey were to determine: (a) the geographic distribution of radiocaesium activity due to fallout from the Chernobyl reactor disaster, (b) the pattern of radiation due to the naturally occurring isotope potassium-40, (c) the activity attributable to caesium-137 fallout from nuclear weapons testing prior to the Chernobyl deposition, (d) the uptake of caesium-137 by vegetation from different soil types. (author)

Agreement between routine electronic hospital discharge and Scottish Stroke Care Audit (SSCA) data in identifying stroke in the Scottish population.

Science.gov (United States)

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.

Integrating cell biology and proteomic approaches in plants.

Science.gov (United States)

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

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

Science.gov (United States)

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.

Genomes to Proteomes

Energy Technology Data Exchange (ETDEWEB)

Panisko, Ellen A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Grigoriev, Igor [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Daly, Don S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Webb-Robertson, Bobbie-Jo [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Baker, Scott E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

2009-03-01

Biologists are awash with genomic sequence data. In large part, this is due to the rapid acceleration in the generation of DNA sequence that occurred as public and private research institutes raced to sequence the human genome. In parallel with the large human genome effort, mostly smaller genomes of other important model organisms were sequenced. Projects following on these initial efforts have made use of technological advances and the DNA sequencing infrastructure that was built for the human and other organism genome projects. As a result, the genome sequences of many organisms are available in high quality draft form. While in many ways this is good news, there are limitations to the biological insights that can be gleaned from DNA sequences alone; genome sequences offer only a bird's eye view of the biological processes endemic to an organism or community. Fortunately, the genome sequences now being produced at such a high rate can serve as the foundation for other global experimental platforms such as proteomics. Proteomic methods offer a snapshot of the proteins present at a point in time for a given biological sample. Current global proteomics methods combine enzymatic digestion, separations, mass spectrometry and database searching for peptide identification. One key aspect of proteomics is the prediction of peptide sequences from mass spectrometry data. Global proteomic analysis uses computational matching of experimental mass spectra with predicted spectra based on databases of gene models that are often generated computationally. Thus, the quality of gene models predicted from a genome sequence is crucial in the generation of high quality peptide identifications. Once peptides are identified they can be assigned to their parent protein. Proteins identified as expressed in a given experiment are most useful when compared to other expressed proteins in a larger biological context or biochemical pathway. In this chapter we will discuss the automatic

Proteomics analysis of alfalfa response to heat stress.

Directory of Open Access Journals (Sweden)

Weimin Li

Full Text Available 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.

Structural and metabolic transitions of C4 leaf development and differentiation defined by microscopy and quantitative proteomics in maize.

Science.gov (United States)

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.

Using patient-reported outcomes in schizophrenia: the Scottish Schizophrenia Outcomes Study.

Science.gov (United States)

Hunter, Robert; Cameron, Rosie; Norrie, John

2009-02-01

The primary aim of the Scottish Schizophrenia Outcomes Study (SSOS) was to assess the feasibility and utility of routinely collecting outcome data in everyday clinical settings. Data were collected over three years in the Scottish National Health Service (NHS). There were two secondary aims of SSOS: first, to compare data from patient-rated, objective, and clinician-rated outcomes, and second, to describe trends in outcome data and service use across Scotland over the three years of the study (2002-2005). This study used a naturalistic, longitudinal, observational cohort design. A representative sample of 1,015 persons with ICD-10 F20-F29 diagnoses (schizophrenia, schizotypal disorders, or delusional disorders) was assessed annually using the clinician-rated measure, the Health of the Nation Outcome Scale (HoNOS), and the patient-reported assessment, the Avon Mental Health Measure (Avon). Objective outcomes data and information on services and interventions were collected. Data were analyzed with regression modeling. Of the 1,015 persons recruited, 78% of the cohort (N=789) completed the study. Over the study period, significant decreases were seen in the number of hospitalizations, incidence of attempted suicide and self-harm, and civil detentions. Avon scores indicated significant improvement on all subscales (behavior, social, access, and mental health) and on the total score. However, HoNOS scores on the behavior and symptom subscales did not change, scores on the impairment subscale increased significantly (indicating increased levels of impairment), and scores on the social subscale decreased significantly (indicating improved social functioning). This study has demonstrated that it is feasible within the Scottish NHS to routinely collect meaningful outcomes data in schizophrenia. Patient-reported assessments were also successfully collected and used in care plans. This model shows that it is possible to incorporate patient-reported assessments into routine

Proteomic explorations of autism spectrum disorder.

Science.gov (United States)

Szoko, Nicholas; McShane, Adam J; Natowicz, Marvin R

2017-09-01

Proteomics, the large-scale study of protein expression in cells and tissues, is a powerful tool to study the biology of clinical conditions and has provided significant insights in many experimental systems. Herein, we review the basics of proteomic methodology and discuss challenges in using proteomic approaches to study autism. Unlike other experimental approaches, such as genomic approaches, there have been few large-scale studies of proteins in tissues from persons with autism. Most of the proteomic studies on autism used blood or other peripheral tissues; few studies used brain tissue. Some studies found dysregulation of aspects of the immune system or of aspects of lipid metabolism, but no consistent findings were noted. Based on the challenges in using proteomics to study autism, we discuss considerations for future studies. Apart from the complex technical considerations implicit in any proteomic analysis, key nontechnical matters include attention to subject and specimen inclusion/exclusion criteria, having adequate sample size to ensure appropriate powering of the study, attention to the state of specimens prior to proteomic analysis, and the use of a replicate set of specimens, when possible. We conclude by discussing some potentially productive uses of proteomics, potentially coupled with other approaches, for future autism research including: (1) proteomic analysis of banked human brain specimens; (2) proteomic analysis of tissues from animal models of autism; and (3) proteomic analysis of induced pluripotent stem cells that are differentiated into various types of brain cells and neural organoids. Autism Res 2017, 10: 1460-1469. © 2017 International Society for Autism Research, Wiley Periodicals, Inc. © 2017 International Society for Autism Research, Wiley Periodicals, Inc.

Proteomics dataset

DEFF Research Database (Denmark)

Bennike, Tue Bjerg; Carlsen, Thomas Gelsing; Ellingsen, Torkell

2017-01-01

patients (Morgan et al., 2012; Abraham and Medzhitov, 2011; Bennike, 2014) [8–10. Therefore, we characterized the proteome of colon mucosa biopsies from 10 inflammatory bowel disease ulcerative colitis (UC) patients, 11 gastrointestinal healthy rheumatoid arthritis (RA) patients, and 10 controls. We...... been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD001608 for ulcerative colitis and control samples, and PXD003082 for rheumatoid arthritis samples....

'If you happen to be the right age, have the right colour, no disability...you're sorted':Social Audit and Equality Policies for staff in Scottish Further Education Colleges

OpenAIRE

Weedon, Elisabet; Riddell, Sheila; Ahlgren, Linda; Litjens, Judith

2008-01-01

This paper focuses on the implications of adopting social audit approaches in order to implement equality policies in Scottish FE colleges, exploring the tension between surface compliance and deep institutional engagement. It provides a brief overview of the Scottish further education context, before turning to a consideration of social audit and equalities within the sector. The data reported comes from a research study funded by the Scottish Further Education Unit which examined college po...

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

Directory of Open Access Journals (Sweden)

Sandeep Chakraborty

2016-05-01

Full Text Available 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.

Advancing cell biology through proteomics in space and time (PROSPECTS)

DEFF Research Database (Denmark)

Lamond, A.I.; Uhlen, M.; Horning, S.

2012-01-01

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...... 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 twinning of Scottish general practices and Malawian clinics: the provision of email and internet services

Directory of Open Access Journals (Sweden)

Ron Neville

2007-01-01

Full Text Available Many patients and health care professionals in the developed world are uncomfortable about doing nothing in the face of the glaring inequities in health care between their own environment and that of Africa. In an effort to 'think global, act local' a Scottish GP practice used personal contacts to build a twinning link with a clinic serving a township in Malawi. This article describes the experience of establishing e-mail and internet services for Malawian health care staff to afford them the same level of access as developed world staff enjoy in accessing educational materials and professional supports. Using our twin link as an exemplar we are now matching other Scottish General Practices to Malawian Clinics around a common theme of modern communication media.

Bruno Braunerde und die Bodentypen - The German-speaking friends of the Scottish soil characters

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Xylem sap proteomics.

Science.gov (United States)

de Bernonville, Thomas Dugé; Albenne, Cécile; Arlat, Matthieu; Hoffmann, Laurent; Lauber, Emmanuelle; Jamet, Elisabeth

2014-01-01

Proteomic analysis of xylem sap has recently become a major field of interest to understand several biological questions related to plant development and responses to environmental clues. The xylem sap appears as a dynamic fluid undergoing changes in its proteome upon abiotic and biotic stresses. Unlike cell compartments which are amenable to purification in sufficient amount prior to proteomic analysis, the xylem sap has to be collected in particular conditions to avoid contamination by intracellular proteins and to obtain enough material. A model plant like Arabidopsis thaliana is not suitable for such an analysis because efficient harvesting of xylem sap is difficult. The analysis of the xylem sap proteome also requires specific procedures to concentrate proteins and to focus on proteins predicted to be secreted. Indeed, xylem sap proteins appear to be synthesized and secreted in the root stele or to originate from dying differentiated xylem cells. This chapter describes protocols to collect xylem sap from Brassica species and to prepare total and N-glycoprotein extracts for identification of proteins by mass spectrometry analyses and bioinformatics.

Farm animal proteomics - A review

DEFF Research Database (Denmark)

Bendixen, Emøke; Danielsen, Marianne; Hollung, Kristin

2011-01-01

In agricultural sciences as in all other areas of life science, the implementation of proteomics and other post-genomic tools is an important step towards more detailed understanding of the complex biological systems that control physiology and pathology of living beings. Farm animals are raised...... and cattle are relevant not only for farm animal sciences, but also for adding to our understanding of complex biological mechanisms of health and disease in humans. The aim of this review is to present an overview of the specific topics of interest within farm animal proteomics, and to highlight some...... of the areas where synergy between classic model organism proteomics and farm animal proteomics is rapidly emerging. Focus will be on introducing the special biological traits that play an important role in food production, and on how proteomics may help optimize farm animal production...

Elucidation of cross-species proteomic effects in human and hominin bone proteome identification through a bioinformatics experiment.

Science.gov (United States)

Welker, F

2018-02-20

The study of ancient protein sequences is increasingly focused on the analysis of older samples, including those of ancient hominins. The analysis of such ancient proteomes thereby potentially suffers from "cross-species proteomic effects": the loss of peptide and protein identifications at increased evolutionary distances due to a larger number of protein sequence differences between the database sequence and the analyzed organism. Error-tolerant proteomic search algorithms should theoretically overcome this problem at both the peptide and protein level; however, this has not been demonstrated. If error-tolerant searches do not overcome the cross-species proteomic issue then there might be inherent biases in the identified proteomes. Here, a bioinformatics experiment is performed to test this using a set of modern human bone proteomes and three independent searches against sequence databases at increasing evolutionary distances: the human (0 Ma), chimpanzee (6-8 Ma) and orangutan (16-17 Ma) reference proteomes, respectively. Incorrectly suggested amino acid substitutions are absent when employing adequate filtering criteria for mutable Peptide Spectrum Matches (PSMs), but roughly half of the mutable PSMs were not recovered. As a result, peptide and protein identification rates are higher in error-tolerant mode compared to non-error-tolerant searches but did not recover protein identifications completely. Data indicates that peptide length and the number of mutations between the target and database sequences are the main factors influencing mutable PSM identification. The error-tolerant results suggest that the cross-species proteomics problem is not overcome at increasing evolutionary distances, even at the protein level. Peptide and protein loss has the potential to significantly impact divergence dating and proteome comparisons when using ancient samples as there is a bias towards the identification of conserved sequences and proteins. Effects are minimized

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

Science.gov (United States)

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…

Diode laser coagulation for the treatment of epistaxis in a Scottish fold cat

Science.gov (United States)

Aoki, Takuma; Madarame, Hiroo; Sugimoto, Keisuke; Sunahara, Hiroshi; Fujii, Yoko; Kanai, Eiichi; Ito, Tetsuro

2015-01-01

We report the case of a 4-year-old, castrated 4.2-kg Scottish fold cat with recurrent epistaxis that was unresponsive to medical therapy. Diathermocoagulation of the nasal mucosa with a diode laser controlled the epistaxis and there was no significant recurrence of epistaxis during 1 year of follow-up. PMID:26130838

Social network architecture of human immune cells unveiled by quantitative proteomics.

Science.gov (United States)

Rieckmann, Jan C; Geiger, Roger; Hornburg, Daniel; Wolf, Tobias; Kveler, Ksenya; Jarrossay, David; Sallusto, Federica; Shen-Orr, Shai S; Lanzavecchia, Antonio; Mann, Matthias; Meissner, Felix

2017-05-01

The immune system is unique in its dynamic interplay between numerous cell types. However, a system-wide view of how immune cells communicate to protect against disease has not yet been established. We applied high-resolution mass-spectrometry-based proteomics to characterize 28 primary human hematopoietic cell populations in steady and activated states at a depth of >10,000 proteins in total. Protein copy numbers revealed a specialization of immune cells for ligand and receptor expression, thereby connecting distinct immune functions. By integrating total and secreted proteomes, we discovered fundamental intercellular communication structures and previously unknown connections between cell types. Our publicly accessible (http://www.immprot.org/) proteomic resource provides a framework for the orchestration of cellular interplay and a reference for altered communication associated with pathology.

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Advances of Proteomic Sciences in Dentistry.

Science.gov (United States)

Khurshid, Zohaib; Zohaib, Sana; Najeeb, Shariq; Zafar, Muhammad Sohail; Rehman, Rabia; Rehman, Ihtesham Ur

2016-05-13

Applications of proteomics tools revolutionized various biomedical disciplines such as genetics, molecular biology, medicine, and dentistry. The aim of this review is to highlight the major milestones in proteomics in dentistry during the last fifteen years. Human oral cavity contains hard and soft tissues and various biofluids including saliva and crevicular fluid. Proteomics has brought revolution in dentistry by helping in the early diagnosis of various diseases identified by the detection of numerous biomarkers present in the oral fluids. This paper covers the role of proteomics tools for the analysis of oral tissues. In addition, dental materials proteomics and their future directions are discussed.

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

Science.gov (United States)

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…

The Mysterious Unfoldome: Structureless, Underappreciated, Yet Vital Part of Any Given Proteome

Directory of Open Access Journals (Sweden)

Vladimir N. Uversky

2010-01-01

Full Text Available Contrarily to the general believe, many biologically active proteins lack stable tertiary and/or secondary structure under physiological conditions in vitro. These intrinsically disordered proteins (IDPs are highly abundant in nature and many of them are associated with various human diseases. The functional repertoire of IDPs complements the functions of ordered proteins. Since IDPs constitute a significant portion of any given proteome, they can be combined in an unfoldome; which is a portion of the proteome including all IDPs (also known as natively unfolded proteins, therefore, unfoldome, and describing their functions, structures, interactions, evolution, and so forth. Amino acid sequence and compositions of IDPs are very different from those of ordered proteins, making possible reliable identification of IDPs at the proteome level by various computational means. Furthermore, IDPs possess a number of unique structural properties and are characterized by a peculiar conformational behavior, including their high stability against low pH and high temperature and their structural indifference toward the unfolding by strong denaturants. These peculiarities were shown to be useful for elaboration of the experimental techniques for the large-scale identification of IDPs in various organisms. Some of the computational and experimental tools for the unfoldome discovery are discussed in this review.

Detection of ROS Induced Proteomic Signatures by Mass Spectrometry

Directory of Open Access Journals (Sweden)

Brian McDonagh

2017-07-01

Full Text Available Reversible and irreversible post-translational modifications (PTMs induced by endogenously generated reactive oxygen species (ROS in regulatory enzymes and proteins plays an essential role in cellular signaling. Almost all cellular processes including metabolism, transcription, translation and degradation have been identified as containing redox regulated proteins. Specific redox modifications of key amino acids generated by ROS offers a dynamic and versatile means to rapidly alter the activity or functional structure of proteins in response to biochemical, environmental, genetic and pathological perturbations. How the proteome responds to these stimuli is of critical importance in oxidant physiology, as it can regulate the cell stress response by reversible and irreversible PTMs, affecting protein activity and protein-protein interactions. Due to the highly labile nature of many ROS species, applying redox proteomics can provide a signature footprint of the ROS species generated. Ideally redox proteomic approaches would allow; (1 the identification of the specific PTM, (2 identification of the amino acid residue that is modified and (3 the percentage of the protein containing the PTM. New developments in MS offer the opportunity of a more sensitive targeted proteomic approach and retrospective data analysis. Subsequent bioinformatics analysis can provide an insight into the biochemical and physiological pathways or cell signaling cascades that are affected by ROS generation. This mini-review will detail current redox proteomic approaches to identify and quantify ROS induced PTMs and the subsequent effects on cellular signaling.

Integration of gel-based and gel-free proteomic data for functional analysis of proteins through Soybean Proteome Database

KAUST Repository

Komatsu, Setsuko

2017-05-10

The Soybean Proteome Database (SPD) stores data on soybean proteins obtained with gel-based and gel-free proteomic techniques. The database was constructed to provide information on proteins for functional analyses. The majority of the data is focused on soybean (Glycine max ‘Enrei’). The growth and yield of soybean are strongly affected by environmental stresses such as flooding. The database was originally constructed using data on soybean proteins separated by two-dimensional polyacrylamide gel electrophoresis, which is a gel-based proteomic technique. Since 2015, the database has been expanded to incorporate data obtained by label-free mass spectrometry-based quantitative proteomics, which is a gel-free proteomic technique. Here, the portions of the database consisting of gel-free proteomic data are described. The gel-free proteomic database contains 39,212 proteins identified in 63 sample sets, such as temporal and organ-specific samples of soybean plants grown under flooding stress or non-stressed conditions. In addition, data on organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored. Furthermore, the database integrates multiple omics data such as genomics, transcriptomics, metabolomics, and proteomics. The SPD database is accessible at http://proteome.dc.affrc.go.jp/Soybean/. Biological significanceThe Soybean Proteome Database stores data obtained from both gel-based and gel-free proteomic techniques. The gel-free proteomic database comprises 39,212 proteins identified in 63 sample sets, such as different organs of soybean plants grown under flooding stress or non-stressed conditions in a time-dependent manner. In addition, organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored in the gel-free proteomics database. A total of 44,704 proteins, including 5490 proteins identified using a gel-based proteomic technique, are stored in the SPD. It accounts for approximately 80% of all

Integration of gel-based and gel-free proteomic data for functional analysis of proteins through Soybean Proteome Database.

Science.gov (United States)

Komatsu, Setsuko; Wang, Xin; Yin, Xiaojian; Nanjo, Yohei; Ohyanagi, Hajime; Sakata, Katsumi

2017-06-23

The Soybean Proteome Database (SPD) stores data on soybean proteins obtained with gel-based and gel-free proteomic techniques. The database was constructed to provide information on proteins for functional analyses. The majority of the data is focused on soybean (Glycine max 'Enrei'). The growth and yield of soybean are strongly affected by environmental stresses such as flooding. The database was originally constructed using data on soybean proteins separated by two-dimensional polyacrylamide gel electrophoresis, which is a gel-based proteomic technique. Since 2015, the database has been expanded to incorporate data obtained by label-free mass spectrometry-based quantitative proteomics, which is a gel-free proteomic technique. Here, the portions of the database consisting of gel-free proteomic data are described. The gel-free proteomic database contains 39,212 proteins identified in 63 sample sets, such as temporal and organ-specific samples of soybean plants grown under flooding stress or non-stressed conditions. In addition, data on organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored. Furthermore, the database integrates multiple omics data such as genomics, transcriptomics, metabolomics, and proteomics. The SPD database is accessible at http://proteome.dc.affrc.go.jp/Soybean/. The Soybean Proteome Database stores data obtained from both gel-based and gel-free proteomic techniques. The gel-free proteomic database comprises 39,212 proteins identified in 63 sample sets, such as different organs of soybean plants grown under flooding stress or non-stressed conditions in a time-dependent manner. In addition, organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored in the gel-free proteomics database. A total of 44,704 proteins, including 5490 proteins identified using a gel-based proteomic technique, are stored in the SPD. It accounts for approximately 80% of all predicted proteins from

Integration of gel-based and gel-free proteomic data for functional analysis of proteins through Soybean Proteome Database

KAUST Repository

Komatsu, Setsuko; Wang, Xin; Yin, Xiaojian; Nanjo, Yohei; Ohyanagi, Hajime; Sakata, Katsumi

2017-01-01

The Soybean Proteome Database (SPD) stores data on soybean proteins obtained with gel-based and gel-free proteomic techniques. The database was constructed to provide information on proteins for functional analyses. The majority of the data is focused on soybean (Glycine max ‘Enrei’). The growth and yield of soybean are strongly affected by environmental stresses such as flooding. The database was originally constructed using data on soybean proteins separated by two-dimensional polyacrylamide gel electrophoresis, which is a gel-based proteomic technique. Since 2015, the database has been expanded to incorporate data obtained by label-free mass spectrometry-based quantitative proteomics, which is a gel-free proteomic technique. Here, the portions of the database consisting of gel-free proteomic data are described. The gel-free proteomic database contains 39,212 proteins identified in 63 sample sets, such as temporal and organ-specific samples of soybean plants grown under flooding stress or non-stressed conditions. In addition, data on organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored. Furthermore, the database integrates multiple omics data such as genomics, transcriptomics, metabolomics, and proteomics. The SPD database is accessible at http://proteome.dc.affrc.go.jp/Soybean/. Biological significanceThe Soybean Proteome Database stores data obtained from both gel-based and gel-free proteomic techniques. The gel-free proteomic database comprises 39,212 proteins identified in 63 sample sets, such as different organs of soybean plants grown under flooding stress or non-stressed conditions in a time-dependent manner. In addition, organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored in the gel-free proteomics database. A total of 44,704 proteins, including 5490 proteins identified using a gel-based proteomic technique, are stored in the SPD. It accounts for approximately 80% of all

Proteomic analysis of purified coronavirus infectious bronchitis virus particles

Directory of Open Access Journals (Sweden)

Shu Dingming

2010-06-01

Full Text Available Abstract Background Infectious bronchitis virus (IBV is the coronavirus of domestic chickens causing major economic losses to the poultry industry. Because of the complexity of the IBV life cycle and the small number of viral structural proteins, important virus-host relationships likely remain to be discovered. Toward this goal, we performed two-dimensional gel electrophoresis fractionation coupled to mass spectrometry identification approaches to perform a comprehensive proteomic analysis of purified IBV particles. Results Apart from the virus-encoded structural proteins, we detected 60 host proteins in the purified virions which can be grouped into several functional categories including intracellular trafficking proteins (20%, molecular chaperone (18%, macromolcular biosynthesis proteins (17%, cytoskeletal proteins (15%, signal transport proteins (15%, protein degradation (8%, chromosome associated proteins (2%, ribosomal proteins (2%, and other function proteins (3%. Interestingly, 21 of the total host proteins have not been reported to be present in virions of other virus families, such as major vault protein, TENP protein, ovalbumin, and scavenger receptor protein. Following identification of the host proteins by proteomic methods, the presence of 4 proteins in the purified IBV preparation was verified by western blotting and immunogold labeling detection. Conclusions The results present the first standard proteomic profile of IBV and may facilitate the understanding of the pathogenic mechanisms.

The proteome of human saliva

Science.gov (United States)

Griffin, Timothy J.

2013-05-01

Human saliva holds tremendous potential for transforming disease and health diagnostics given its richness of molecular information and non-invasive collection. Enumerating its molecular constituents is an important first step towards reaching this potential. Among the molecules in saliva, proteins and peptides arguably have the most value: they can directly indicate biochemical functions linked to a health condition/disease state, and they are attractive targets for biomarker assay development. However, cataloging and defining the human salivary proteome is challenging given the dynamic, chemically heterogeneous and complex nature of the system. In addition, the overall human saliva proteome is composed of several "sub-proteomes" which include: intact full length proteins, proteins carrying post-translational modifications (PTMs), low molecular weight peptides, and the metaproteome, derived from protein products from nonhuman organisms (e.g. microbes) present in the oral cavity. Presented here will be a summary of communal efforts to meet the challenge of characterizing the multifaceted saliva proteome, focusing on the use of mass spectrometry as the proteomic technology of choice. Implications of these efforts to characterize the salivary proteome in the context of disease diagnostics will also be discussed.

Elucidation of cross-species proteomic effects in human and hominin bone proteome identification through a bioinformatics experiment

DEFF Research Database (Denmark)

Welker, F.

2018-01-01

Background: The study of ancient protein sequences is increasingly focused on the analysis of older samples, including those of ancient hominins. The analysis of such ancient proteomes thereby potentially suffers from "cross-species proteomic effects": the loss of peptide and protein identificati......Background: The study of ancient protein sequences is increasingly focused on the analysis of older samples, including those of ancient hominins. The analysis of such ancient proteomes thereby potentially suffers from "cross-species proteomic effects": the loss of peptide and protein...... not been demonstrated. If error-tolerant searches do not overcome the cross-species proteomic issue then there might be inherent biases in the identified proteomes. Here, a bioinformatics experiment is performed to test this using a set of modern human bone proteomes and three independent searches against......), but roughly half of the mutable PSMs were not recovered. As a result, peptide and protein identification rates are higher in error-tolerant mode compared to non-error-tolerant searches but did not recover protein identifications completely. Data indicates that peptide length and the number of mutations...

Genetic epidemiology of motor neuron disease-associated variants in the Scottish population.

Science.gov (United States)

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.

Exploring the Arabidopsis Proteome: Influence of Protein Solubilization Buffers on Proteome Coverage

KAUST Repository

Marondedze, Claudius; Wong, Aloysius Tze; Groen, Arnoud; Serano, Natalia Lorena Gorron; Jankovic, Boris R.; Lilley, Kathryn; Gehring, Christoph A; Thomas, Ludivine

2014-01-01

The study of proteomes provides new insights into stimulus-specific responses of protein synthesis and turnover, and the role of post-translational modifications at the systems level. Due to the diverse chemical nature of proteins and shortcomings in the analytical techniques used in their study, only a partial display of the proteome is achieved in any study, and this holds particularly true for plant proteomes. Here we show that different solubilization and separation methods have profound effects on the resulting proteome. In particular, we observed that the type of detergents employed in the solubilization buffer preferentially enriches proteins in different functional categories. These include proteins with a role in signaling, transport, response to temperature stimuli and metabolism. This data may offer a functional bias on comparative analysis studies. In order to obtain a broader coverage, we propose a two-step solubilization protocol with first a detergent-free buffer and then a second step utilizing a combination of two detergents to solubilize proteins.

Exploring the Arabidopsis Proteome: Influence of Protein Solubilization Buffers on Proteome Coverage

Directory of Open Access Journals (Sweden)

Claudius Marondedze

2014-12-01

Full Text Available The study of proteomes provides new insights into stimulus-specific responses of protein synthesis and turnover, and the role of post-translational modifications at the systems level. Due to the diverse chemical nature of proteins and shortcomings in the analytical techniques used in their study, only a partial display of the proteome is achieved in any study, and this holds particularly true for plant proteomes. Here we show that different solubilization and separation methods have profound effects on the resulting proteome. In particular, we observed that the type of detergents employed in the solubilization buffer preferentially enriches proteins in different functional categories. These include proteins with a role in signaling, transport, response to temperature stimuli and metabolism. This data may offer a functional bias on comparative analysis studies. In order to obtain a broader coverage, we propose a two-step solubilization protocol with first a detergent-free buffer and then a second step utilizing a combination of two detergents to solubilize proteins.

Exploring the Arabidopsis Proteome: Influence of Protein Solubilization Buffers on Proteome Coverage

KAUST Repository

Marondedze, Claudius

2014-12-31

The study of proteomes provides new insights into stimulus-specific responses of protein synthesis and turnover, and the role of post-translational modifications at the systems level. Due to the diverse chemical nature of proteins and shortcomings in the analytical techniques used in their study, only a partial display of the proteome is achieved in any study, and this holds particularly true for plant proteomes. Here we show that different solubilization and separation methods have profound effects on the resulting proteome. In particular, we observed that the type of detergents employed in the solubilization buffer preferentially enriches proteins in different functional categories. These include proteins with a role in signaling, transport, response to temperature stimuli and metabolism. This data may offer a functional bias on comparative analysis studies. In order to obtain a broader coverage, we propose a two-step solubilization protocol with first a detergent-free buffer and then a second step utilizing a combination of two detergents to solubilize proteins.

Bank stability as a risk factor for pipeline infrastructure: a Scottish example

Science.gov (United States)

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

Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage.

Science.gov (United States)

Van, Phu T; Schmid, Amy K; King, Nichole L; Kaur, Amardeep; Pan, Min; Whitehead, Kenia; Koide, Tie; Facciotti, Marc T; Goo, Young Ah; Deutsch, Eric W; Reiss, David J; Mallick, Parag; Baliga, Nitin S

2008-09-01

The relatively small numbers of proteins and fewer possible post-translational modifications in microbes provide a unique opportunity to comprehensively characterize their dynamic proteomes. We have constructed a PeptideAtlas (PA) covering 62.7% of the predicted proteome of the extremely halophilic archaeon Halobacterium salinarum NRC-1 by compiling approximately 636 000 tandem mass spectra from 497 mass spectrometry runs in 88 experiments. Analysis of the PA with respect to biophysical properties of constituent peptides, functional properties of parent proteins of detected peptides, and performance of different mass spectrometry approaches has highlighted plausible strategies for improving proteome coverage and selecting signature peptides for targeted proteomics. Notably, discovery of a significant correlation between absolute abundances of mRNAs and proteins has helped identify low abundance of proteins as the major limitation in peptide detection. Furthermore, we have discovered that iTRAQ labeling for quantitative proteomic analysis introduces a significant bias in peptide detection by mass spectrometry. Therefore, despite identifying at least one proteotypic peptide for almost all proteins in the PA, a context-dependent selection of proteotypic peptides appears to be the most effective approach for targeted proteomics.

Scottish economic bulletin

International Nuclear Information System (INIS)

1993-01-01

The evidence of recovery in the United Kingdom (UK) economy, which had tentatively emerged in the second half of 1992, became stronger in the first half of this year. Examination of the components of total final demand shows that the UK has a longstanding preference to consume rather than to save and invest. Government policy in the 1990s will seek to create the conditions in which this balance can be altered. Given that consumer spending accounts for over half of final demand, the behaviour of the consumer remains a key determinant of the timing and strength of economic recovery. Data for the service sector in Scotland show that employment levels have held up much better than in Great Britain as a whole, although there is some evidence of the later impact of the recession on Scotland. The short-term prospects for the Scottish economy continue to be critically dependent on the export sector, given the depreciation of sterling since the suspension of exchange rate mechanism (ERM) membership, the fall in short-term UK interest rates and the continued improvement in relative manufacturing unit costs. The principal worry concerns the demand prospects in Scotland's major export markets, especially in Europe. Most independent economic forecasters expect that gross domestic product (GDP) growth in Scotland will be below that of the UK in 1993 and 1994. However, the unemployment rate is expected to remain lower in Scotland than in the UK over this period. (author)

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

Science.gov (United States)

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…

Concurrency and climate change signal in Scottish flooding

Science.gov (United States)

Harding, A. E.; Butler, A.; Goody, N.; Bertram, D.; Baggaley, N.; Tett, S. F.

2013-12-01

The Scottish Environment Protection Agency maintains a database of river gauging stations and intensity rain-gauges with a 3-hourly resolution that covers the majority of Scotland. Both SEPA and a number of other Scottish agencies are invested in climate change attribution in this data set. SEPA's main interest lies in trend detection and changes in river level (';stage') data throughout Scotland. Emergency response teams are more concerned with the concurrency of multiple flood events that might stretch their ability to respond effectively. Unfortunately, much of the rainfall signal within SEPA's river-gauge data is altered by land use changes, modified by artificial interventions such as reservoirs, compromised by tidal flow, or obscured by measurement issues. Data reduction techniques, indices of extreme rainfall, and hydrology-driven discrimination have been employed to produce a reduced set of flood-relevant information for 24-hour ';flashy' events. Links between this set and North Atlantic circulation have been explored, as have patterns of mutual occurrence across Scotland and location- and seasonally- dependent trends through time. Both frontal systems and summer convective storms have been characterised in terms of subsequent flood-inducing flow regime, their changing behaviour over the last fifty years, and their spatial extent. This is the first stage of an ongoing project that will intelligently expand to take less robust river and rain-gauge stations into account through statistical analysis and hydrological modelling. It is also the first study of its type to analyse a nation-scale dataset of both rainfall and river flow from multiple catchments for flood event concurrency. As rainfall events are expected to intensify across much of Europe, this kind of research is likely to have an increasing degree of relevance for policy-makers. This project demonstrates that productive, policy-relevant and mutually-rewarding partnerships are already underway.

Network-based analysis of proteomic profiles

KAUST Repository

Wong, Limsoon

2016-01-26

Mass spectrometry (MS)-based proteomics is a widely used and powerful tool for profiling systems-wide protein expression changes. It can be applied for various purposes, e.g. biomarker discovery in diseases and study of drug responses. Although RNA-based high-throughput methods have been useful in providing glimpses into the underlying molecular processes, the evidences they provide are indirect. Furthermore, RNA and corresponding protein levels have been known to have poor correlation. On the other hand, MS-based proteomics tend to have consistency issues (poor reproducibility and inter-sample agreement) and coverage issues (inability to detect the entire proteome) that need to be urgently addressed. In this talk, I will discuss how these issues can be addressed by proteomic profile analysis techniques that use biological networks (especially protein complexes) as the biological context. In particular, I will describe several techniques that we have been developing for network-based analysis of proteomics profile. And I will present evidence that these techniques are useful in identifying proteomics-profile analysis results that are more consistent, more reproducible, and more biologically coherent, and that these techniques allow expansion of the detected proteome to uncover and/or discover novel proteins.

Proteomic profiling of the human T-cell nucleolus.

Science.gov (United States)

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.

Arabidopsis peroxisome proteomics

Directory of Open Access Journals (Sweden)

John D. Bussell

2013-04-01

Full Text Available The analytical depth of investigation of the peroxisomal proteome of the model plant Arabidopsis thaliana has not yet reached that of other major cellular organelles such as chloroplasts or mitochondria. This is primarily due to the difficulties associated with isolating and obtaining purified samples of peroxisomes from Arabidopsis. So far only a handful of research groups have been successful in obtaining such fractions. To make things worse, enriched peroxisome fractions frequently suffer from significant organellar contamination, lowering confidence in localization assignment of the identified proteins. As with other cellular compartments, identification of peroxisomal proteins forms the basis for investigations of the dynamics of the peroxisomal proteome. It is therefore not surprising that, in terms of functional analyses by proteomic means, there remains a considerable gap between peroxisomes and chloroplasts or mitochondria. Alternative strategies are needed to overcome the obstacle of hard-to-obtain organellar fractions. This will help to close the knowledge gap between peroxisomes and other organelles and provide a full picture of the physiological pathways shared between organelles. In this review we briefly summarize the status quo and discuss some of the methodological alternatives to classic organelle proteomic approaches.

ScottishPower learning's school-to-work education and training programs[Empowering socially excluded youth and building future managers' leadership, communication and social skills

Energy Technology Data Exchange (ETDEWEB)

Kitagawa, K.; Watt, D.; Yachnin, R.

2001-08-01

Serving approximately 7 million homes and businesses across the United Kingdom and the northwest United States, ScottishPower and its subsidiaries are one of the 12 largest electricity groups in the world. Following deregulation in the electricity industry in the United Kingdom in 1990, ScottishPower found it had to change quickly to capture emerging opportunities. It recognized the need to support employee development and set up an Open Learning Centre to be used by staff for their own personal development. Investment was made in occupational health and wellness services. The following three-step training process was established for ScottishPower: (1) conduct employability assessments; (2) design and deliver a learning activity so that the individual will be successful in the workplace; and (3) engage learners. ScottishPower has implemented several training programs to empower employees, their families and their communities: education transition programs for 15-18 year olds; pre-vocational training for 16-25 year olds; and, vocational training for 16-25 year olds. The keys to success include people, processes, infrastructure, resources committed, challenges, and innovation. In cooperation with trade unions, government bodies, economic development agencies and education and training agencies, ScottishPower has developed a wide spectrum of training and development programs aimed at unemployed young people in socially deprived areas of the United Kingdom.

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

Science.gov (United States)

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 ).

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Proteomics Insights into Autophagy.

Science.gov (United States)

Cudjoe, Emmanuel K; Saleh, Tareq; Hawkridge, Adam M; Gewirtz, David A

2017-10-01

Autophagy, a conserved cellular process by which cells recycle their contents either to maintain basal homeostasis or in response to external stimuli, has for the past two decades become one of the most studied physiological processes in cell biology. The 2016 Nobel Prize in Medicine and Biology awarded to Dr. Ohsumi Yoshinori, one of the first scientists to characterize this cellular mechanism, attests to its importance. The induction and consequent completion of the process of autophagy results in wide ranging changes to the cellular proteome as well as the secretome. MS-based proteomics affords the ability to measure, in an unbiased manner, the ubiquitous changes that occur when autophagy is initiated and progresses in the cell. The continuous improvements and advances in mass spectrometers, especially relating to ionization sources and detectors, coupled with advances in proteomics experimental design, has made it possible to study autophagy, among other process, in great detail. Innovative labeling strategies and protein separation techniques as well as complementary methods including immuno-capture/blotting/staining have been used in proteomics studies to provide more specific protein identification. In this review, we will discuss recent advances in proteomics studies focused on autophagy. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

[Impact of the Italian smoking ban and comparison with the evaluation of the Scottish ban].

Science.gov (United States)

Gorini, Giuseppe

2011-01-01

The Italian smoking ban entered into force on January 10th, 2005, and banned smoking from enclosed workplaces and hospitality premises (HPs), even though provided separated smoking areas. Actually, only 1-2%of HPs built these areas, while no figures are available on the prevalence of smoking rooms in workplaces other than HPs. Italians were more in favour of the law after the ban. In 2008 Italians were the Europeans most in favour of a national smoking ban (88%). Measurements of environmental nicotine and particulate matter with a diameter hospitality sector against the ban in 2004, no studies on impact of the ban on hospitality industry businesses were conducted in Italy. We used the conceptual model for the evaluation of the impact of smoke-free policies, proposed by the International Agency for Research on Cancer (IARC), to compare Italian and Scottish evaluations of the bans. The Scottish evaluation was planned some years before the implementation, and was based on a network of researchers of different disciplines. The quantification of decrease in second-hand smoke (SHS) exposure in the general population and in hospitality workers was one of the main objectives of the Scottish evaluation. The Italian evaluation devoted more attention to distal (reduction of hospital admissions) and incidental effects of the law (trend in smoking prevalence, cigarette consumption). Qualitative studies in bars, homes, and communities recording changes in attitudes on tobacco smoking after the introduction of the ban, were conducted only in Scotland. In Italy the main problem was to develop and fund a network of researchers involved on a shared evaluation plan.

Subregion-Specific Proteomic Signature in the Hippocampus for Recognition Processes in Adult Mice

Directory of Open Access Journals (Sweden)

Lukas M. von Ziegler

2018-03-01

Full Text Available Summary: The hippocampal formation is a brain structure essential for higher-order cognitive functions. It has a complex anatomical organization and cellular composition, and hippocampal subregions have different properties and functional roles. In this study, we used SWATH-MS to determine whether the proteomes of hippocampus areas CA1 and CA3 can explain the commonalities or specificities of these subregions in basal conditions and after recognition memory. We show that the proteomes of areas CA1 and CA3 are largely different in basal conditions and that differential changes and dynamics in protein expression are induced in these areas after recognition of an object or object location. While changes are consistent across both recognition paradigms in area CA1, they are not in area CA3, suggesting distinct proteomic responses in areas CA1 and CA3 for memory formation. : How does the proteome differ in hippocampus areas CA1 and CA3? von Ziegler et al. identify the proteomes of areas CA1 and CA3 and characterize their dynamics during different recognition processes in adult mice. Keywords: hippocampus, areas CA1 and CA3, proteome, dynamics, object memory, object location memory, mass spectrometry, SWATH-MS, mice, bioinformatic tools

[Progress in stable isotope labeled quantitative proteomics methods].

Science.gov (United States)

Zhou, Yuan; Shan, Yichu; Zhang, Lihua; Zhang, Yukui

2013-06-01

Quantitative proteomics is an important research field in post-genomics era. There are two strategies for proteome quantification: label-free methods and stable isotope labeling methods which have become the most important strategy for quantitative proteomics at present. In the past few years, a number of quantitative methods have been developed, which support the fast development in biology research. In this work, we discuss the progress in the stable isotope labeling methods for quantitative proteomics including relative and absolute quantitative proteomics, and then give our opinions on the outlook of proteome quantification methods.

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

Science.gov (United States)

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.

NIH Common Fund - Disruptive Proteomics Technologies - Challenges and Opportunities | Office of Cancer Clinical Proteomics Research

Science.gov (United States)

This Request for Information (RFI) is directed toward determining how best to accelerate research in disruptive proteomics technologies. The Disruptive Proteomics Technologies (DPT) Working Group of the NIH Common Fund wishes to identify gaps and opportunities in current technologies and methodologies related to proteome-wide measurements.  For the purposes of this RFI, “disruptive” is defined as very rapid, very significant gains, similar to the "disruptive" technology development that occurred in DNA sequencing technology.

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

Science.gov (United States)

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…

A decade of proteomics accomplished! Central and Eastern European Proteomic Conference (CEEPC) celebrates its 10th Anniversary in Budapest, Hungary.

Science.gov (United States)

Gadher, Suresh Jivan; Drahos, László; Vékey, Károly; Kovarova, Hana

2017-07-01

The Central and Eastern European Proteomic Conference (CEEPC) proudly celebrated its 10th Anniversary with an exciting scientific program inclusive of proteome, proteomics and systems biology in Budapest, Hungary. Since 2007, CEEPC has represented 'state-of the-art' proteomics in and around Central and Eastern Europe and these series of conferences have become a well-recognized event in the proteomic calendar. Fresher challenges and global healthcare issues such as ageing and chronic diseases are driving clinical and scientific research towards regenerative, reparative and personalized medicine. To this end, proteomics may enable diverse intertwining research fields to reach their end goals. CEEPC will endeavor to facilitate these goals.

Scottish Campaign to Resist the Atomic Menace annual report 1992/93

International Nuclear Information System (INIS)

1993-01-01

In a year which saw the Scottish Campaign to Resist the Atomic Menace (SCRAM) Safe Energy journal reach its 15th birthday, the Earth Summit in Rio was amongst the most important events. Though this historic international meeting failed to live up to the expectations of many, it was a step in the right direction. The activities of the many non-governmental organisations was particularly encouraging, and their continuing work on climate change in particular could be vital. The nuclear industry persists in claiming green credentials, but it has not had a good year. For SCRAM, founded to oppose the Torness nuclear power station, the Public Inquiry in December into Scottish Nuclear's plans for a dry store was of particular significance. Our pragmatic decision not to oppose the scheme did not go unnoticed. We were happy to provide registered objectors with information, including our report on dry storage. Having reached a landmark of fifteen years continuous publication, Safe Energy continues to be well received by a readership which includes concerned individuals, campaigners, politicians, environmentalists, government agencies, the media and the nuclear industry. SCRAM's main role is dissemination of information, and the journal is our main vehicle. We aim to deal with complex issues in a readable way, and are encouraged that such a broad range of people find it of use. (author)

Mediterranean-type diet and brain structural change from 73 to 76 years in a Scottish cohort

Science.gov (United States)

Corley, Janie; Cox, Simon R.; Valdés Hernández, Maria C.; Craig, Leone C.A.; Dickie, David Alexander; Karama, Sherif; McNeill, Geraldine M.; Bastin, Mark E.; Wardlaw, Joanna M.; Deary, Ian J.

2017-01-01

Objective: To assess the association between Mediterranean-type diet (MeDi) and change in brain MRI volumetric measures and mean cortical thickness across a 3-year period in older age (73–76 years). Methods: We focused on 2 longitudinal brain volumes (total and gray matter; n = 401 and 398, respectively) plus a longitudinal measurement of cortical thickness (n = 323), for which the previous cross-sectional evidence of an association with the MeDi was strongest. Adherence to the MeDi was calculated from data gathered from a food frequency questionnaire at age 70, 3 years prior to the baseline imaging data collection. Results: In regression models adjusting for relevant demographic and physical health indicators, we found that lower adherence to the MeDi was associated with greater 3-year reduction in total brain volume (explaining 0.5% of variance, p Scottish cohort is predictive of total brain atrophy over a 3-year interval. Fish and meat consumption does not drive this change, suggesting that other components of the MeDi or, possibly, all of its components in combination are responsible for the association. PMID:28053008

Proteome reference map of Drosophila melanogaster head.

Science.gov (United States)

Lee, Tian-Ren; Huang, Shun-Hong; Lee, Chi-Ching; Lee, Hsiao-Yun; Chan, Hsin-Tzu; Lin, Kuo-Sen; Chan, Hong-Lin; Lyu, Ping-Chiang

2012-06-01

Drosophila melanogaster has been used as a genetic model organism to understand the fundamental molecular mechanisms in human biology including memory formation that has been reported involving protein synthesis and/or post-translational modification. In this study, we employed a proteomic platform based on fluorescent 2DE and MALDI-TOF MS to build a standard D. melanogaster head proteome map for proteome-proteome comparison. In order to facilitate the comparison, an interactive database has been constructed for systematically integrating and analyzing the proteomes from different conditions and further implicated to study human diseases related to D. melanogaster model. In summary, the fundamental head proteomic database and bioinformatic analysis will be useful for further elucidating the biological mechanisms such as memory formation and neurodegenerative diseases. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Skeletal muscle proteomics: current approaches, technical challenges and emerging techniques

LENUS (Irish Health Repository)

Ohlendieck, Kay

2011-02-01

Abstract Background Skeletal muscle fibres represent one of the most abundant cell types in mammals. Their highly specialised contractile and metabolic functions depend on a large number of membrane-associated proteins with very high molecular masses, proteins with extensive posttranslational modifications and components that exist in highly complex supramolecular structures. This makes it extremely difficult to perform conventional biochemical studies of potential changes in protein clusters during physiological adaptations or pathological processes. Results Skeletal muscle proteomics attempts to establish the global identification and biochemical characterisation of all members of the muscle-associated protein complement. A considerable number of proteomic studies have employed large-scale separation techniques, such as high-resolution two-dimensional gel electrophoresis or liquid chromatography, and combined them with mass spectrometry as the method of choice for high-throughput protein identification. Muscle proteomics has been applied to the comprehensive biochemical profiling of developing, maturing and aging muscle, as well as the analysis of contractile tissues undergoing physiological adaptations seen in disuse atrophy, physical exercise and chronic muscle transformation. Biomedical investigations into proteome-wide alterations in skeletal muscle tissues were also used to establish novel biomarker signatures of neuromuscular disorders. Importantly, mass spectrometric studies have confirmed the enormous complexity of posttranslational modifications in skeletal muscle proteins. Conclusions This review critically examines the scientific impact of modern muscle proteomics and discusses its successful application for a better understanding of muscle biology, but also outlines its technical limitations and emerging techniques to establish new biomarker candidates.

Proteomics in pulmonary research: selected methodical aspects

Directory of Open Access Journals (Sweden)

Martin Petrek

2007-10-01

Full Text Available Recent years witness rapid expansion of applications of proteomics to clinical research including non-malignant lung disorders. These developments bring along the need for standardisation of proteomic experiments. This paper briefly reviews basic methodical aspects of appliedproteomic studies using SELDI-TOF mass spectrometry platform as example but also emphasizes general aspects of quality assurance in proteomics. Key-words: lung proteome, quality assurance, SELDI-TOF MS

The impact of oil on the Scottish economy with particular reference to the Aberdeen economy

International Nuclear Information System (INIS)

Lloyd, M.G.; Newlands, D.A.

1992-01-01

The establishment of the North Sea oil industry over the last 20 years has had far reaching and dramatic effects upon the whole Scottish economy but especially upon those areas where oil related activity is geographically concentrated. This chapter discusses the impact of oil on the Scottish economy with particular reference to developments in the Aberdeen area. It is comprised of five main sections. The first outlines the way in which the oil industry has developed in Britain, noting that, despite rapid growth, there have been many lost opportunities. The impact of oil related developments in Scotland is discussed next before the focus narrows to the Aberdeen economy. The third section describes the familiar benefits of oil developments in Aberdeen while the fourth section analyses some of the less familiar costs. Finally, there is some discussion of the way in which the gains and losses of oil developments in Aberdeen have been distributed. (author)

The potato tuber mitochondrial proteome

DEFF Research Database (Denmark)

Salvato, Fernanda; Havelund, Jesper Foged; Chen, Mingjie

2014-01-01

Mitochondria are called the powerhouses of the cell. To better understand the role of mitochondria in maintaining and regulating metabolism in storage tissues, highly purified mitochondria were isolated from dormant potato tubers (Solanum tuberosum 'Folva') and their proteome investigated. Proteins...... manner using normalized spectral counts including as many as 5-fold more "extreme" proteins (low mass, high isoelectric point, hydrophobic) than previous mitochondrial proteome studies. We estimate that this compendium of proteins represents a high coverage of the potato tuber mitochondrial proteome...

Developments in emergency planning within Scottish nuclear

International Nuclear Information System (INIS)

Simpson, A.

2000-01-01

Scottish Nuclear has recently completed a major program of improvements to its nuclear emergency facilities. The improvements include the construction of a purpose built Off-Site Emergency Centre for each of its two power stations and the development of a computer based information management system to facilitate the rapid distribution of information on an emergency to local, regional and national agencies. A computer code has also been developed to allow the rapid assessment of the effects of any accidental release on the local population. The improvements to the emergency facilities have been coupled with changes in local and national arrangements for dealing with a civil nuclear emergency. The use of airborne surveying techniques for rapidly determining levels of deposited activity following an accident is also being examined and preliminary airborne surveys have been carried out. (author)

Gardening is beneficial for adult mental health: Scottish Health Survey, 2012-2013.

Science.gov (United States)

Shiue, Ivy

2016-07-01

Gardening has been reported as being beneficial for mental well-being for vulnerable populations since 2000. However, little is known concerning its role in the general population. Therefore, the aim of the present study was to investigate the relationship of gardening and mental health in adults in a countrywide and population-based setting. Data was retrieved from and analysed in the Scottish Health Survey, 2012-2013. Information on demographics, lifestyle factors, gardening engagement, and adult mental health by General Health Questionnaire was obtained by household interview. Statistical analyses including chi-square test, t-test and survey-weighted logistic and multi-nominal regression modelling were performed. Of 9709 Scottish adults aged 16-99, 5 531 (57.0%) people did not do any gardening or building work in the last four weeks. A total of 888 (9.2%) people reported poor self-rated health. Gardening was associated with adult mental health in people both with or without heart conditions including ability to concentrate, feeling playing a useful part in things, feeling capable of making decisions, thinking of self as worthless, feeling reasonably happy, etc. General adults with or without heart conditions could benefit from engaging with gardening or building work. Future public health programmes promoting such activity should be encouraged in order to optimise adult mental health.

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

Science.gov (United States)

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.

Risk, risk conflicts, sub-politics and social and environmental accounting and accountability in Scottish salmon farming

NARCIS (Netherlands)

Georgakopoulos, G.; Thomson, I.

2008-01-01

Purpose To offer a theoretical analysis, inspired by contemporary research into risk, of the social and environmental accounting processes observed in an empirical study on Scottish salmon farming. Methodology / Approach This paper used a Grounded Theory approach. Empirical evidence was collected on

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

Science.gov (United States)

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.…

Ethnic variations in upper gastrointestinal hospitalizations and deaths: the Scottish Health and Ethnicity Linkage Study.

Science.gov (United States)

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.

Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation

DEFF Research Database (Denmark)

Chen, Ke; Gao, Ye; Mih, Nathan

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 prin...

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

Science.gov (United States)

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

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

Science.gov (United States)

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.

Proteomic Analysis of Chinese Hamster Ovary Cells

DEFF Research Database (Denmark)

Baycin-Hizal, Deniz; Tabb, David L.; Chaerkady, Raghothama

2012-01-01

To complement the recent genomic sequencing of Chinese hamster ovary (CHO) cells, proteomic analysis was performed on CHO cells including the cellular proteome, secretome, and glycoproteome using tandem mass spectrometry (MS/MS) of multiple fractions obtained from gel electrophoresis, multidimens......To complement the recent genomic sequencing of Chinese hamster ovary (CHO) cells, proteomic analysis was performed on CHO cells including the cellular proteome, secretome, and glycoproteome using tandem mass spectrometry (MS/MS) of multiple fractions obtained from gel electrophoresis...

Semen proteomics and male infertility.

Science.gov (United States)

Jodar, Meritxell; Soler-Ventura, Ada; Oliva, Rafael

2017-06-06

Semen is a complex body fluid containing an admixture of spermatozoa suspended in secretions from the testes and epididymis which are mixed at the time of ejaculation with secretions from other accessory sex glands such as the prostate and seminal vesicles. High-throughput technologies have revealed that, contrary to the idea that sperm cells are simply a silent delivery vehicle of the male genome to the oocyte, the sperm cells in fact provide both a specific epigenetically marked DNA together with a complex population of proteins and RNAs crucial for embryogenesis. Similarly, -omic technologies have also enlightened that seminal fluid seems to play a much greater role than simply being a medium to carry the spermatozoa through the female reproductive tract. In the present review, we briefly overview the sperm cell biology, consider the key issues in sperm and seminal fluid sample preparation for high-throughput proteomic studies, describe the current state of the sperm and seminal fluid proteomes generated by high-throughput proteomic technologies and provide new insights into the potential communication between sperm and seminal fluid. In addition, comparative proteomic studies open a window to explore the potential pathogenic mechanisms of infertility and the discovery of potential biomarkers with clinical significance. The review updates the numerous proteomics studies performed on semen, including spermatozoa and seminal fluid. In addition, an integrative analysis of the testes, sperm and seminal fluid proteomes is also included providing insights into the molecular mechanisms that regulate the generation, maturation and transit of spermatozoa. Furthermore, the compilation of several differential proteomic studies focused on male infertility reveals potential pathways disturbed in specific subtypes of male infertility and points out towards future research directions in the field. Copyright © 2016 Elsevier B.V. All rights reserved.

Progress on the HUPO Draft Human Proteome: 2017 Metrics of the Human Proteome Project.

Science.gov (United States)

Omenn, Gilbert S; Lane, Lydie; Lundberg, Emma K; Overall, Christopher M; Deutsch, Eric W

2017-12-01

The Human Proteome Organization (HUPO) Human Proteome Project (HPP) continues to make progress on its two overall goals: (1) completing the protein parts list, with an annual update of the HUPO draft human proteome, and (2) making proteomics an integrated complement to genomics and transcriptomics throughout biomedical and life sciences research. neXtProt version 2017-01-23 has 17 008 confident protein identifications (Protein Existence [PE] level 1) that are compliant with the HPP Guidelines v2.1 ( https://hupo.org/Guidelines ), up from 13 664 in 2012-12 and 16 518 in 2016-04. Remaining to be found by mass spectrometry and other methods are 2579 "missing proteins" (PE2+3+4), down from 2949 in 2016. PeptideAtlas 2017-01 has 15 173 canonical proteins, accounting for nearly all of the 15 290 PE1 proteins based on MS data. These resources have extensive data on PTMs, single amino acid variants, and splice isoforms. The Human Protein Atlas v16 has 10 492 highly curated protein entries with tissue and subcellular spatial localization of proteins and transcript expression. Organ-specific popular protein lists have been generated for broad use in quantitative targeted proteomics using SRM-MS or DIA-SWATH-MS studies of biology and disease.

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

Science.gov (United States)

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.

The Silver Darlings: An Emblem of the Scottish Sea and History

OpenAIRE

Berton-Charrière, Danièle

2017-01-01

From the Middle Ages onwards, herring—one of the most used marine resources—has provided Scotland with a precious, cheap, plentiful and nutritious source of food. Fishing was first a subsistence activity, and it then developed into an industry. Once in unbelievable abundance—the Old German word ‘herring’ means ‘multitude’—herring attracted thousands of boats from all over Europe to the Scottish waters, and at the peak of the herring boom, Britain exported a quarter of a million tonnes a year....

Plutonium and americium in arctic waters, the North Sea and Scottish and Irish coastal zones

DEFF Research Database (Denmark)

Hallstadius, L.; Aarkrog, Asker; Dahlgaard, Henning

1986-01-01

Plutonium and americium have been measured in surface waters of the Greenland and Barents Seas and in the northern North Sea from 1980 through 1984. Measurements in water and biota, Fucus, Mytilus and Patella, were carried out in North-English and Scottish waters in 1982 and Fucus samples were co...

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

Science.gov (United States)

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…

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

Science.gov (United States)

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.

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

Science.gov (United States)

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 (pcancer 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 (pcancer 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

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

Science.gov (United States)

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 (ptanning (p=0.009) and sunburn (pskin 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 (ptan made them feel better about themselves (pskin 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.

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

Directory of Open Access Journals (Sweden)

Andrew Watterson

2018-04-01

Full Text Available 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.

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

Science.gov (United States)

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

Low-Impact Exploration for Gold in the Scottish Caledonides.

Science.gov (United States)

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.

How much of the difference in life expectancy between Scottish cities does deprivation explain?

Science.gov (United States)

Seaman, R; Mitchell, R; Dundas, R; Leyland, A H; Popham, F

2015-10-16

Glasgow's low life expectancy and high levels of deprivation are well documented. Studies comparing Glasgow to similarly deprived cities in England suggest an excess of deaths in Glasgow that cannot be accounted for by deprivation. Within Scotland comparisons are more equivocal suggesting deprivation could explain Glasgow's excess mortality. Few studies have used life expectancy, an intuitive measure that quantifies the between-city difference in years. This study aimed to use the most up-to-date data to compare Glasgow to other Scottish cities and to (i) evaluate whether deprivation could account for lower life expectancy in Glasgow and (ii) explore whether the age distribution of mortality in Glasgow could explain its lower life expectancy. Sex specific life expectancy was calculated for 2007-2011 for the population in Glasgow and the combined population of Aberdeen, Dundee and Edinburgh. Life expectancy was calculated for deciles of income deprivation, based on the national ranking of datazones, using the Scottish Index of Multiple Deprivation. Life expectancy in Glasgow overall, and by deprivation decile, was compared to that in Aberdeen, Dundee and Edinburgh combined, and the life expectancy difference decomposed by age using Arriaga's discrete method. Life expectancy for the whole Glasgow population was lower than the population of Aberdeen, Dundee and Edinburgh combined. When life expectancy was compared by national income deprivation decile, Glasgow's life expectancy was not systematically lower, and deprivation accounted for over 90 % of the difference. This was reduced to 70 % of the difference when carrying out sensitivity analysis using city-specific income deprivation deciles. In both analyses life expectancy was not systematically lower in Glasgow when stratified by deprivation. Decomposing the differences in life expectancy also showed that the age distribution of mortality was not systematically different in Glasgow after accounting for deprivation

Proteomic approaches in brain research and neuropharmacology.

Science.gov (United States)

Vercauteren, Freya G G; Bergeron, John J M; Vandesande, Frans; Arckens, Lut; Quirion, Rémi

2004-10-01

Numerous applications of genomic technologies have enabled the assembly of unprecedented inventories of genes, expressed in cells under specific physiological and pathophysiological conditions. Complementing the valuable information generated through functional genomics with the integrative knowledge of protein expression and function should enable the development of more efficient diagnostic tools and therapeutic agents. Proteomic analyses are particularly suitable to elucidate posttranslational modifications, expression levels and protein-protein interactions of thousands of proteins at a time. In this review, two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) investigations of brain tissues in neurodegenerative diseases such as Alzheimer's disease, Down syndrome and schizophrenia, and the construction of 2D-PAGE proteome maps of the brain are discussed. The role of the Human Proteome Organization (HUPO) as an international coordinating organization for proteomic efforts, as well as challenges for proteomic technologies and data analysis are also addressed. It is expected that the use of proteomic strategies will have significant impact in neuropharmacology over the coming decade.

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

Czech Academy of Sciences Publication Activity Database

Gadher, S. J.; Marczak, L.; Luczak, M.; Stobiecki, M.; Widlak, P.; Kovářová, Hana

2016-01-01

Roč. 13, č. 1 (2016), s. 5-7 ISSN 1478-9450. [Central and Eastern European Proteomic Conference (CEEPC) /9./. Poznaň, 15.06.2015-18.06.2015] Institutional support: RVO:67985904 Keywords : Central and Eastern Proteomic Conference * proteomics * mass spectrometry imaging Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.849, year: 2016

Applying mass spectrometry-based qualitative proteomics to human amygdaloid complex

Directory of Open Access Journals (Sweden)

Joaquín eFernández-Irigoyen

2014-03-01

Full Text Available The amygdaloid complex is a key brain structure involved in the expression of behaviours and emotions such as learning, fear, and anxiety. Brain diseases including depression, epilepsy, autism, schizophrenia, and Alzheimer`s disease, have been associated with amygdala dysfunction. For several decades, neuroanatomical, neurophysiological, volumetric, and cognitive approaches have been the gold standard techniques employed to characterize the amygdala functionality. However, little attention has been focused specifically on the molecular composition of the human amygdala from the perspective of proteomics. We have performed a global proteome analysis employing protein and peptide fractionation methods followed by nano-liquid chromatography tandem mass spectrometry (nanoLC-MS/MS, detecting expression of at least 1820 protein species in human amygdala, corresponding to 1814 proteins which represent a 9-fold increase in proteome coverage with respect to previous proteomic profiling of the rat amygdala. Gene ontology analysis were used to determine biological process represented in human amygdala highlighting molecule transport, nucleotide binding, and oxidoreductase and GTPase activities. Bioinformatic analyses have revealed that nearly 4% of identified proteins have been previously associated to neurodegenerative syndromes, and 26% of amygdaloid proteins were also found to be present in cerebrospinal fluid (CSF. In particular, a subset of amygdaloid proteins was mainly involved in axon guidance, synaptic vesicle release, L1CAM interactome, and signaling pathways transduced by NGF and NCAM1. Taken together, our data contributes to the repertoire of the human brain proteome, serving as a reference library to provide basic information for understanding the neurobiology of the human amygdala.

Proteomic properties reveal phyloecological clusters of Archaea.

Directory of Open Access Journals (Sweden)

Nela Nikolic

Full Text Available In this study, we propose a novel way to describe the variety of environmental adaptations of Archaea. We have clustered 57 Archaea by using a non-redundant set of proteomic features, and verified that the clusters correspond to environmental adaptations to the archaeal habitats. The first cluster consists dominantly of hyperthermophiles and hyperthermoacidophilic aerobes. The second cluster joins together halophilic and extremely halophilic Archaea, while the third cluster contains mesophilic (mostly methanogenic Archaea together with thermoacidophiles. The non-redundant subset of proteomic features was found to consist of five features: the ratio of charged residues to uncharged, average protein size, normalized frequency of beta-sheet, normalized frequency of extended structure and number of hydrogen bond donors. We propose this clustering to be termed phyloecological clustering. This approach could give additional insights into relationships among archaeal species that may be hidden by sole phylogenetic analysis.

Ethnic Variations in Liver- and Alcohol-Related Disease Hospitalisations and Mortality: The Scottish Health and Ethnicity Linkage Study.

Science.gov (United States)

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

Establishing Substantial Equivalence: Proteomics

Science.gov (United States)

Lovegrove, Alison; Salt, Louise; Shewry, Peter R.

Wheat is a major crop in world agriculture and is consumed after processing into a range of food products. It is therefore of great importance to determine the consequences (intended and unintended) of transgenesis in wheat and whether genetically modified lines are substantially equivalent to those produced by conventional plant breeding. Proteomic analysis is one of several approaches which can be used to address these questions. Two-dimensional PAGE (2D PAGE) remains the most widely available method for proteomic analysis, but is notoriously difficult to reproduce between laboratories. We therefore describe methods which have been developed as standard operating procedures in our laboratory to ensure the reproducibility of proteomic analyses of wheat using 2D PAGE analysis of grain proteins.

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

Science.gov (United States)

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…

Proteome identification of the silkworm middle silk gland

Directory of Open Access Journals (Sweden)

Jian-ying Li

2016-03-01

Full Text Available To investigate the functional differentiation among the anterior (A, middle (M, and posterior (P regions of silkworm middle silk gland (MSG, their proteomes were characterized by shotgun LC–MS/MS analysis with a LTQ-Orbitrap mass spectrometer. To get better proteome identification and quantification, triplicate replicates of mass spectrometry analysis were performed for each sample. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (Vizcaíno et al., 2014 [1] via the PRIDE partner repository (Vizcaino, 2013 [2] with the dataset identifier http://www.ebi.ac.uk/pride/archive/projects/PXD003371. The peptide identifications that were further processed by PeptideProphet program in Trans-Proteomic Pipeline (TPP after database search with Mascot software were also available in .XML format files. Data presented here are related to a research article published in Journal of Proteomics by Li et al. (2015 [3]. Keywords: Bombyx mori, Middle silk gland, Silk protein synthesis, Shotgun proteomics, Label-free

A comprehensive proteomics study on platelet concentrates: Platelet proteome, storage time and Mirasol pathogen reduction technology.

Science.gov (United States)

Salunkhe, Vishal; De Cuyper, Iris M; Papadopoulos, Petros; van der Meer, Pieter F; Daal, Brunette B; Villa-Fajardo, María; de Korte, Dirk; van den Berg, Timo K; Gutiérrez, Laura

2018-03-19

Platelet concentrates (PCs) represent a blood transfusion product with a major concern for safety as their storage temperature (20-24°C) allows bacterial growth, and their maximum storage time period (less than a week) precludes complete microbiological testing. Pathogen inactivation technologies (PITs) provide an additional layer of safety to the blood transfusion products from known and unknown pathogens such as bacteria, viruses, and parasites. In this context, PITs, such as Mirasol Pathogen Reduction Technology (PRT), have been developed and are implemented in many countries. However, several studies have shown in vitro that Mirasol PRT induces a certain level of platelet shape change, hyperactivation, basal degranulation, and increased oxidative damage during storage. It has been suggested that Mirasol PRT might accelerate what has been described as the platelet storage lesion (PSL), but supportive molecular signatures have not been obtained. We aimed at dissecting the influence of both variables, that is, Mirasol PRT and storage time, at the proteome level. We present comprehensive proteomics data analysis of Control PCs and PCs treated with Mirasol PRT at storage days 1, 2, 6, and 8. Our workflow was set to perform proteomics analysis using a gel-free and label-free quantification (LFQ) approach. Semi-quantification was based on LFQ signal intensities of identified proteins using MaxQuant/Perseus software platform. Data are available via ProteomeXchange with identifier PXD008119. We identified marginal differences between Mirasol PRT and Control PCs during storage. However, those significant changes at the proteome level were specifically related to the functional aspects previously described to affect platelets upon Mirasol PRT. In addition, the effect of Mirasol PRT on the platelet proteome appeared not to be exclusively due to an accelerated or enhanced PSL. In summary, semi-quantitative proteomics allows to discern between proteome changes due to

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

Science.gov (United States)

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

Proteome-wide analysis and diel proteomic profiling of the cyanobacterium Arthrospira platensis PCC 8005.

Directory of Open Access Journals (Sweden)

Sabine Matallana-Surget

Full Text Available The filamentous cyanobacterium Arthrospira platensis has a long history of use as a food supply and it has been used by the European Space Agency in the MELiSSA project, an artificial microecosystem which supports life during long-term manned space missions. This study assesses progress in the field of cyanobacterial shotgun proteomics and light/dark diurnal cycles by focusing on Arthrospira platensis. Several fractionation workflows including gel-free and gel-based protein/peptide fractionation procedures were used and combined with LC-MS/MS analysis, enabling the overall identification of 1306 proteins, which represents 21% coverage of the theoretical proteome. A total of 30 proteins were found to be significantly differentially regulated under light/dark growth transition. Interestingly, most of the proteins showing differential abundance were related to photosynthesis, the Calvin cycle and translation processes. A novel aspect and major achievement of this work is the successful improvement of the cyanobacterial proteome coverage using a 3D LC-MS/MS approach, based on an immobilized metal affinity chromatography, a suitable tool that enabled us to eliminate the most abundant protein, the allophycocyanin. We also demonstrated that cell growth follows a light/dark cycle in A. platensis. This preliminary proteomic study has highlighted new characteristics of the Arthrospira platensis proteome in terms of diurnal regulation.

Comparison of protein extraction methods suitable for proteomics ...

African Journals Online (AJOL)

Jane

2011-07-27

Jul 27, 2011 ... An efficient protein extraction method is a prerequisite for successful implementation of proteomics. ... research, it is noteworthy to discover a proteome ..... Proteomic analysis of rice (Oryza sativa) seeds during germination.

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

Science.gov (United States)

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

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

Science.gov (United States)

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.

Validation of an imaging based cardiovascular risk score in a Scottish population.

Science.gov (United States)

Kockelkoren, Remko; Jairam, Pushpa M; Murchison, John T; Debray, Thomas P A; Mirsadraee, Saeed; van der Graaf, Yolanda; Jong, Pim A de; van Beek, Edwin J R

2018-01-01

A radiological risk score that determines 5-year cardiovascular disease (CVD) risk using routine care CT and patient information readily available to radiologists was previously developed. External validation in a Scottish population was performed to assess the applicability and validity of the risk score in other populations. 2915 subjects aged ≥40 years who underwent routine clinical chest CT scanning for non-cardiovascular diagnostic indications were followed up until first diagnosis of, or death from, CVD. Using a case-cohort approach, all cases and a random sample of 20% of the participant's CT examinations were visually graded for cardiovascular calcifications and cardiac diameter was measured. The radiological risk score was determined using imaging findings, age, gender, and CT indication. Performance on 5-year CVD risk prediction was assessed. 384 events occurred in 2124 subjects during a mean follow-up of 4.25 years (0-6.4 years). The risk score demonstrated reasonable performance in the studied population. Calibration showed good agreement between actual and 5-year predicted risk of CVD. The c-statistic was 0.71 (95%CI:0.67-0.75). The radiological CVD risk score performed adequately in the Scottish population offering a potential novel strategy for identifying patients at high risk for developing cardiovascular disease using routine care CT data. Copyright © 2017 Elsevier B.V. All rights reserved.

Urine Proteomics in the Era of Mass Spectrometry

Directory of Open Access Journals (Sweden)

Ashley Beasley-Green

2016-11-01

Full Text Available With the technological advances of mass spectrometry (MS-based platforms, clinical proteomics is one of the most rapidly growing areas in biomedical research. Urine proteomics has become a popular subdiscipline of clinical proteomics because it is an ideal source for the discovery of noninvasive disease biomarkers. The urine proteome offers a comprehensive view of the local and systemic physiology since the proteome is primarily composed of proteins/peptides from the kidneys and plasma. The emergence of MS-based proteomic platforms as prominent bioanalytical tools in clinical applications has enhanced the identification of protein-based urinary biomarkers. This review highlights the characteristics of urine that make it an attractive biofluid for biomarker discovery and the impact of MS-based technologies on the clinical assessment of urinary protein biomarkers.

Tobacco Retail Environments and Social Inequalities in Individual-Level Smoking and Cessation Among Scottish Adults.

Science.gov (United States)

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.

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

Science.gov (United States)

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…

Proteomics of Plant Pathogenic Fungi

Directory of Open Access Journals (Sweden)

Raquel González-Fernández

2010-01-01

Full Text Available Plant pathogenic fungi cause important yield losses in crops. In order to develop efficient and environmental friendly crop protection strategies, molecular studies of the fungal biological cycle, virulence factors, and interaction with its host are necessary. For that reason, several approaches have been performed using both classical genetic, cell biology, and biochemistry and the modern, holistic, and high-throughput, omic techniques. This work briefly overviews the tools available for studying Plant Pathogenic Fungi and is amply focused on MS-based Proteomics analysis, based on original papers published up to December 2009. At a methodological level, different steps in a proteomic workflow experiment are discussed. Separate sections are devoted to fungal descriptive (intracellular, subcellular, extracellular and differential expression proteomics and interactomics. From the work published we can conclude that Proteomics, in combination with other techniques, constitutes a powerful tool for providing important information about pathogenicity and virulence factors, thus opening up new possibilities for crop disease diagnosis and crop protection.

Trends in bullying victimization in Scottish adolescents 1994-2014: changing associations with mental well-being.

Science.gov (United States)

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.

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

Science.gov (United States)

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.

The Scottish Government's Rural and Environmental Science and Analytical Services Strategic Research Progamme

Science.gov (United States)

Dawson, Lorna; Bestwick, Charles

2013-04-01

The Strategic Research Programme focuses on the delivery of outputs and outcomes within the major policy agenda areas of climate change, land use and food security, and to impact on the 'Wealthier', 'Healthier' and 'Greener' strategic objectives of the Scottish Government. The research is delivered through two programmes: 'Environmental Change' and 'Food, Land and People'; the core strength of which is the collaboration between the Scottish Government's Main Research Providers-The James Hutton Institute, the Moredun Research Institute, Rowett Institute of Nutrition and Health University of Aberdeen, Scotland's Rural College, Biomathematics and Statistics Scotland and The Royal Botanic Gardens Edinburgh. The research actively seeks to inform and be informed by stakeholders from policy, farming, land use, water and energy supply, food production and manufacturing, non-governmental organisations, voluntary organisations, community groups and general public. This presentation will provide an overview of the programme's interdisciplinary research, through examples from across the programme's themes. Examples will exemplify impact within the Strategic Programme's priorities of supporting policy and practice, contributing to economic growth and innovation, enhancing collaborative and multidisciplinary research, growing scientific resilience and delivering scientific excellence. http://www.scotland.gov.uk/Topics/Research/About/EBAR/StrategicResearch/future-research-strategy/Themes/ http://www.knowledgescotland.org/news.php?article_id=295

Edinburgh, the Scottish pioneers of anatomy and their lasting influence in South Africa.

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Quantitative Proteomics Reveals Temporal Proteomic Changes in Signaling Pathways during BV2 Mouse Microglial Cell Activation.

Science.gov (United States)

Woo, Jongmin; Han, Dohyun; Wang, Joseph Injae; Park, Joonho; Kim, Hyunsoo; Kim, Youngsoo

2017-09-01

The development of systematic proteomic quantification techniques in systems biology research has enabled one to perform an in-depth analysis of cellular systems. We have developed a systematic proteomic approach that encompasses the spectrum from global to targeted analysis on a single platform. We have applied this technique to an activated microglia cell system to examine changes in the intracellular and extracellular proteomes. Microglia become activated when their homeostatic microenvironment is disrupted. There are varying degrees of microglial activation, and we chose to focus on the proinflammatory reactive state that is induced by exposure to such stimuli as lipopolysaccharide (LPS) and interferon-gamma (IFN-γ). Using an improved shotgun proteomics approach, we identified 5497 proteins in the whole-cell proteome and 4938 proteins in the secretome that were associated with the activation of BV2 mouse microglia by LPS or IFN-γ. Of the differentially expressed proteins in stimulated microglia, we classified pathways that were related to immune-inflammatory responses and metabolism. Our label-free parallel reaction monitoring (PRM) approach made it possible to comprehensively measure the hyper-multiplex quantitative value of each protein by high-resolution mass spectrometry. Over 450 peptides that corresponded to pathway proteins and direct or indirect interactors via the STRING database were quantified by label-free PRM in a single run. Moreover, we performed a longitudinal quantification of secreted proteins during microglial activation, in which neurotoxic molecules that mediate neuronal cell loss in the brain are released. These data suggest that latent pathways that are associated with neurodegenerative diseases can be discovered by constructing and analyzing a pathway network model of proteins. Furthermore, this systematic quantification platform has tremendous potential for applications in large-scale targeted analyses. The proteomics data for

Virtual Labs in proteomics: new E-learning tools.

Science.gov (United States)

Ray, Sandipan; Koshy, Nicole Rachel; Reddy, Panga Jaipal; Srivastava, Sanjeeva

2012-05-17

Web-based educational resources have gained enormous popularity recently and are increasingly becoming a part of modern educational systems. Virtual Labs are E-learning platforms where learners can gain the experience of practical experimentation without any direct physical involvement on real bench work. They use computerized simulations, models, videos, animations and other instructional technologies to create interactive content. Proteomics being one of the most rapidly growing fields of the biological sciences is now an important part of college and university curriculums. Consequently, many E-learning programs have started incorporating the theoretical and practical aspects of different proteomic techniques as an element of their course work in the form of Video Lectures and Virtual Labs. To this end, recently we have developed a Virtual Proteomics Lab at the Indian Institute of Technology Bombay, which demonstrates different proteomics techniques, including basic and advanced gel and MS-based protein separation and identification techniques, bioinformatics tools and molecular docking methods, and their applications in different biological samples. This Tutorial will discuss the prominent Virtual Labs featuring proteomics content, including the Virtual Proteomics Lab of IIT-Bombay, and E-resources available for proteomics study that are striving to make proteomic techniques and concepts available and accessible to the student and research community. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 14). Details can be found at: http://www.proteomicstutorials.org/. Copyright © 2012 Elsevier B.V. All rights reserved.

Analysis of mass spectrometry data in proteomics

DEFF Research Database (Denmark)

Matthiesen, Rune; Jensen, Ole N

2008-01-01

The systematic study of proteins and protein networks, that is, proteomics, calls for qualitative and quantitative analysis of proteins and peptides. Mass spectrometry (MS) is a key analytical technology in current proteomics and modern mass spectrometers generate large amounts of high-quality data...... that in turn allow protein identification, annotation of secondary modifications, and determination of the absolute or relative abundance of individual proteins. Advances in mass spectrometry-driven proteomics rely on robust bioinformatics tools that enable large-scale data analysis. This chapter describes...... some of the basic concepts and current approaches to the analysis of MS and MS/MS data in proteomics....

Urine sample preparation for proteomic analysis.

Science.gov (United States)

Olszowy, Pawel; Buszewski, Boguslaw

2014-10-01

Sample preparation for both environmental and more importantly biological matrices is a bottleneck of all kinds of analytical processes. In the case of proteomic analysis this element is even more important due to the amount of cross-reactions that should be taken into consideration. The incorporation of new post-translational modifications, protein hydrolysis, or even its degradation is possible as side effects of proteins sample processing. If protocols are evaluated appropriately, then identification of such proteins does not bring difficulties. However, if structural changes are provided without sufficient attention then protein sequence coverage will be reduced or even identification of such proteins could be impossible. This review summarizes obstacles and achievements in protein sample preparation of urine for proteome analysis using different tools for mass spectrometry analysis. The main aim is to present comprehensively the idea of urine application as a valuable matrix. This article is dedicated to sample preparation and application of urine mainly in novel cancer biomarkers discovery. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Directory of Open Access Journals (Sweden)

Kim Kyung

2011-05-01

Full Text Available Abstract 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

Knowledge Translation: Moving Proteomics Science to Innovation in Society.

Science.gov (United States)

Holmes, Christina; McDonald, Fiona; Jones, Mavis; Graham, Janice

2016-06-01

Proteomics is one of the pivotal next-generation biotechnologies in the current "postgenomics" era. Little is known about the ways in which innovative proteomics science is navigating the complex socio-political space between laboratory and society. It cannot be assumed that the trajectory between proteomics laboratory and society is linear and unidirectional. Concerned about public accountability and hopes for knowledge-based innovations, funding agencies and citizens increasingly expect that emerging science and technologies, such as proteomics, are effectively translated and disseminated as innovation in society. Here, we describe translation strategies promoted in the knowledge translation (KT) and science communication literatures and examine the use of these strategies within the field of proteomics. Drawing on data generated from qualitative interviews with proteomics scientists and ethnographic observation of international proteomics conferences over a 5-year period, we found that proteomics science incorporates a variety of KT strategies to reach knowledge users outside the field. To attain the full benefit of KT, however, proteomics scientists must challenge their own normative assumptions and approaches to innovation dissemination-beyond the current paradigm relying primarily on publication for one's scientific peers within one's field-and embrace the value of broader (interdisciplinary) KT strategies in promoting the uptake of their research. Notably, the Human Proteome Organization (HUPO) is paying increasing attention to a broader range of KT strategies, including targeted dissemination, integrated KT, and public outreach. We suggest that increasing the variety of KT strategies employed by proteomics scientists is timely and would serve well the omics system sciences community.

First systematic plant proteomics workshop in Botany Department, University of Delhi: transferring proteomics knowledge to next-generation researchers and students.

Science.gov (United States)

Deswal, Renu; Abat, Jasmeet Kaur; Sehrawat, Ankita; Gupta, Ravi; Kashyap, Prakriti; Sharma, Shruti; Sharma, Bhavana; Chaurasia, Satya Prakash; Chanu, Sougrakpam Yaiphabi; Masi, Antonio; Agrawal, Ganesh Kumar; Sarkar, Abhijit; Agrawal, Raj; Dunn, Michael J; Renaut, Jenny; Rakwal, Randeep

2014-07-01

International Plant Proteomics Organization (INPPO) outlined ten initiatives to promote plant proteomics in each and every country. With greater emphasis in developing countries, one of those was to "organize workshops at national and international levels to train manpower and exchange information". This third INPPO highlights covers the workshop organized for the very first time in a developing country, India, at the Department of Botany in University of Delhi on December 26-30, 2013 titled - "1(st) Plant Proteomics Workshop / Training Program" under the umbrella of INPPO India-Nepal chapter. Selected 20 participants received on-hand training mainly on gel-based proteomics approach along with manual booklet and parallel lectures on this and associated topics. In house, as well as invited experts drawn from other Universities and Institutes (national and international), delivered talks on different aspects of gel-based and gel-free proteomics. Importance of gel-free proteomics approach, translational proteomics, and INPPO roles were presented and interactively discussed by a group of three invited speakers Drs. Ganesh Kumar Agrawal (Nepal), Randeep Rakwal (Japan), and Antonio Masi (Italy). Given the output of this systematic workshop, it was proposed and thereafter decided to be organized every alternate year; the next workshop will be held in 2015. Furthermore, possibilities on providing advanced training to those students / researchers / teachers with basic knowledge in proteomics theory and experiments at national and international levels were discussed. INPPO is committed to generating next-generation trained manpower in proteomics, and it would only happen by the firm determination of scientists to come forward and do it. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Proteomics methods applied to malaria: Plasmodium falciparum

International Nuclear Information System (INIS)

Cuesta Astroz, Yesid; Segura Latorre, Cesar

2012-01-01

Malaria is a parasitic disease that has a high impact on public health in developing countries. The sequencing of the plasmodium falciparum genome and the development of proteomics have enabled a breakthrough in understanding the biology of the parasite. Proteomics have allowed to characterize qualitatively and quantitatively the parasite s expression of proteins and has provided information on protein expression under conditions of stress induced by antimalarial. Given the complexity of their life cycle, this takes place in the vertebrate host and mosquito vector. It has proven difficult to characterize the protein expression during each stage throughout the infection process in order to determine the proteome that mediates several metabolic, physiological and energetic processes. Two dimensional electrophoresis, liquid chromatography and mass spectrometry have been useful to assess the effects of antimalarial on parasite protein expression and to characterize the proteomic profile of different p. falciparum stages and organelles. The purpose of this review is to present state of the art tools and advances in proteomics applied to the study of malaria, and to present different experimental strategies used to study the parasite's proteome in order to show the advantages and disadvantages of each one.

Factors associated with self-reported first sexual intercourse in Scottish adolescents

Directory of Open Access Journals (Sweden)

van Teijlingen Edwin R

2009-03-01

Full Text Available Abstract Background There is continuing concern about high pregnancy rates and increasing numbers of sexually transmitted infections being detected in Scottish adolescents. Consistent evidence about factors associated with risky sexual behaviours, including early first sexual intercourse, may help to identify adolescents at risk and help improve interventions. This study aimed to provide detailed analysis of the evidence of the associations between individual factors and early sexual intercourse using cross-sectional questionnaire data from 4,379 Scottish adolescents who participated in a sexual health intervention evaluation. Findings Multivariate secondary analysis showed that aspects of family and school life such as decreasing parental monitoring (OR 1.45, 95% CI 1.24–1.70 and decreasing enjoyment of school (OR 2.55, 95% CI 2.15–3.03 were associated with reporting previous sexual intercourse. Furthermore, females were more likely to report previous sexual intercourse than males (OR 1.48, 95% CI 1.14–1.91. Several factors commonly used to inform sexual health intervention design, such as socioeconomic status, self-esteem and religion, were not independently associated. Conclusion These results contribute to the evidence base for the association of several factors with early initiation of sexual activity. The findings suggest that interventions aiming to delay first intercourse may need to consider targeting aspects of individuals' connection to their school and family. Furthermore, the results do not support the need to consider socio-economic background, religion or self-esteem of the individuals in intervention design.

The Seed Proteome Web Portal

Directory of Open Access Journals (Sweden)

Marc eGalland

2012-06-01

Full Text Available The Seed Proteome Web Portal (SPWP; http://www.seedproteome.com/ gives access to information both on quantitative seed proteomic data and on seed-related protocols. Firstly, the SPWP provides access to the 475 different Arabidopsis seed proteins annotated from 2 dimensional electrophoresis (2DE maps. Quantitative data are available for each protein according to their accumulation profile during the germination process. These proteins can be retrieved either in list format or directly on scanned 2DE maps. These proteomic data reveal that 40% of seed proteins maintain a stable abundance over germination, up to radicle protrusion. During sensu stricto germination (24 h upon imbibition about 50% of the proteins display quantitative variations, exhibiting an increased abundance (35% or a decreasing abundance (15%. Moreover, during radicle protrusion (24 h to 48 h upon imbibition, 41% proteins display quantitative variations with an increased (23% or a decreasing abundance (18%. In addition, an analysis of the seed proteome revealed the importance of protein post-translational modifications as demonstrated by the poor correlation (r2 = 0.29 between the theoretical (predicted from Arabidopsis genome and the observed protein isoelectric points. Secondly, the SPWP is a relevant technical resource for protocols specifically dedicated to Arabidopsis seed proteome studies. Concerning 2D electrophoresis, the user can find efficient procedures for sample preparation, electrophoresis coupled with gel analysis and protein identification by mass spectrometry, which we have routinely used during the last 12 years. Particular applications such as the detection of oxidized proteins or de novo synthetized proteins radiolabeled by [35S]-methionine are also given in great details. Future developments of this portal will include proteomic data from studies such as dormancy release and protein turnover through de novo protein synthesis analyses during germination.

The broccoli (Brassica oleracea) phloem tissue proteome.

Science.gov (United States)

Anstead, James A; Hartson, Steven D; Thompson, Gary A

2013-11-07

The transport of sugars, hormones, amino acids, proteins, sugar alcohols, and other organic compounds from the sites of synthesis to the sites of use or storage occurs through the conducting cells of the phloem. To better understand these processes a comprehensive understanding of the proteins involved is required. While a considerable amount of data has been obtained from proteomic analyses of phloem sap, this has mainly served to identify the soluble proteins that are translocated through the phloem network. In order to obtain more comprehensive proteomic data from phloem tissue we developed a simple dissection procedure to isolate phloem tissue from Brassica oleracea. The presence of a high density of phloem sieve elements was confirmed using light microscopy and fluorescently labeled sieve element-specific antibodies. To increase the depth of the proteomic analysis for membrane bound and associated proteins, soluble proteins were extracted first and subsequent extractions were carried out using two different detergents (SDS and CHAPSO). Across all three extractions almost four hundred proteins were identified and each extraction method added to the analysis demonstrating the utility of an approach combining several extraction protocols. The phloem was found to be enriched in proteins associated with biotic and abiotic stress responses and structural proteins. Subsequent expression analysis identified a number of genes that appear to be expressed exclusively or at very high levels in phloem tissue, including genes that are known to express specifically in the phloem as well as novel phloem genes.

Comparative proteomics of matrix fractions between pimpled and normal chicken eggshells.

Science.gov (United States)

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

Global Proteome Analysis of Leptospira interrogans

Science.gov (United States)

Comparative global proteome analyses were performed on Leptospira interrogans serovar Copenhageni grown under conventional in vitro conditions and those mimicking in vivo conditions (iron limitation and serum presence). Proteomic analyses were conducted using iTRAQ and LC-ESI-tandem mass spectrometr...

Is there a "Scottish effect" for self reports of health? Individual level analysis of the 2001 UK census

Directory of Open Access Journals (Sweden)

Popham Frank

2006-07-01

Full Text Available Abstract Background Scotland's overall health record is comparatively poor for a Western European country, particularly amongst people of working age. A number of previous studies have explored why this might be the case by comparing mortality in Scotland with England and Wales. A study in the 1980s showed that the higher prevalence of deprivation in Scotland accounted for Scotland's excess mortality risk. However, more recent studies suggest that deprivation now explains less of this excess. This has led to the suggestion that there is a yet unidentified "Scottish effect" contributing to Scotland's mortality excess. Recent research has also suggested that there could be an unidentified effect influencing Scotland's higher rate of heart disease. This paper explores whether there is also an unexplained Scottish excess, relative to England, in self reports of poor health. Methods Data came from the individual Sample of Anonymised Records, a 3% random sample of the 2001 UK census. Using logistic regression models, self reports of health (limiting illness and general health from the working age populations (aged 25 to 64 of Scotland and England were compared. Account was taken of people's country of birth. Stratified analysis by employment status allowed further exploration of Scotland's excess. Results People born and living in Scotland reported higher levels of poor general health and limiting illness compared to people born and living in England. Adjustment for socioeconomic position and employment status largely explained the higher rates. In the stratified analysis a Scottish excess was seen only amongst the economically inactive born and living in Scotland. For those in employment, people born and living in Scotland actually had slightly lower odds of reporting poor general health and limiting illness than people born and living in England. Conclusion This analysis suggests that higher rates of poor self reported health in Scotland can be

Complications following incident stroke resulting in readmissions: an analysis of data from three Scottish health surveys.

Science.gov (United States)

Ponomarev, Dmitry; Miller, Claire; Govan, Lindsay; Haig, Caroline; Wu, Olivia; Langhorne, Peter

2015-08-01

Stroke is widely recognized as the major contributor to morbidity and mortality in the United Kingdom. We analyzed the data obtained from the three consecutive Scottish Health Surveys and the Scottish Morbidity records, with the aim of identifying risk factors for, and timing of, common poststroke complications. There were 19434 individuals sampled during three Scottish Health Surveys in 1995, 1998, and 2001. For these individuals their morbidity and mortality outcomes were obtained in 2007. Incident stroke prevalence, risk factors for a range of poststroke complications, and average times until such complications in the sample were established. Of the total of 168 incident stroke admissions (0·86% of the survey), 16·1% people died during incident stroke hospitalization. Of the remaining 141 stroke survivors, 75·2% were rehospitalized at least once. The most frequent reason for readmission after stroke was a cardiovascular complication (28·6%), median time until event 1412 days, followed by infection (17·3%, median 1591 days). The risk of cardiovascular readmission was higher in those with 'poor' self-assessed health (odds ratio 7·70; 95% confidence interval 1·64-43·27), smokers (odds ratio 4·24; 95% confidence interval 1·11-21·59), and doubled with every five years increase in age (odds ratio 1·97; 95% confidence interval 1·46-2·65). 'Poor' self-assessed health increased chance of readmission for infection (odds ratio 14·11; 95% confidence interval 2·27-276·56). Cardiovascular events and infections are the most frequent poststroke complications resulting in readmissions. The time period until event provides a possibility to focus monitoring on those people at risk of readmission and introduce preventative measures, thereby reducing readmission-associated costs. © 2013 The Authors. International Journal of Stroke © 2013 World Stroke Organization.

Marine proteomics: a critical assessment of an emerging technology.

Science.gov (United States)

Slattery, Marc; Ankisetty, Sridevi; Corrales, Jone; Marsh-Hunkin, K Erica; Gochfeld, Deborah J; Willett, Kristine L; Rimoldi, John M

2012-10-26

The application of proteomics to marine sciences has increased in recent years because the proteome represents the interface between genotypic and phenotypic variability and, thus, corresponds to the broadest possible biomarker for eco-physiological responses and adaptations. Likewise, proteomics can provide important functional information regarding biosynthetic pathways, as well as insights into mechanism of action, of novel marine natural products. The goal of this review is to (1) explore the application of proteomics methodologies to marine systems, (2) assess the technical approaches that have been used, and (3) evaluate the pros and cons of this proteomic research, with the intent of providing a critical analysis of its future roles in marine sciences. To date, proteomics techniques have been utilized to investigate marine microbe, plant, invertebrate, and vertebrate physiology, developmental biology, seafood safety, susceptibility to disease, and responses to environmental change. However, marine proteomics studies often suffer from poor experimental design, sample processing/optimization difficulties, and data analysis/interpretation issues. Moreover, a major limitation is the lack of available annotated genomes and proteomes for most marine organisms, including several "model species". Even with these challenges in mind, there is no doubt that marine proteomics is a rapidly expanding and powerful integrative molecular research tool from which our knowledge of the marine environment, and the natural products from this resource, will be significantly expanded.

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

Science.gov (United States)

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…

Delivering Formal Outdoor Learning in Protected Areas: A Case Study of Scottish Natural Heritage National Nature Reserves

Science.gov (United States)

Black, Rosemary

2013-01-01

In most countries, protected area management agencies provide formal outdoor learning opportunities for a wide range of educational groups. For high-quality formal outdoor learning programmes that provide a range of experiences to be effectively delivered, specific resources and infrastructure are needed. Using the case study of Scottish Natural…

Proteogenomics Dashboard for the Human Proteome Project.

Science.gov (United States)

Tabas-Madrid, Daniel; Alves-Cruzeiro, Joao; Segura, Victor; Guruceaga, Elizabeth; Vialas, Vital; Prieto, Gorka; García, Carlos; Corrales, Fernando J; Albar, Juan Pablo; Pascual-Montano, Alberto

2015-09-04

dasHPPboard is a novel proteomics-based dashboard that collects and reports the experiments produced by the Spanish Human Proteome Project consortium (SpHPP) and aims to help HPP to map the entire human proteome. We have followed the strategy of analog genomics projects like the Encyclopedia of DNA Elements (ENCODE), which provides a vast amount of data on human cell lines experiments. The dashboard includes results of shotgun and selected reaction monitoring proteomics experiments, post-translational modifications information, as well as proteogenomics studies. We have also processed the transcriptomics data from the ENCODE and Human Body Map (HBM) projects for the identification of specific gene expression patterns in different cell lines and tissues, taking special interest in those genes having little proteomic evidence available (missing proteins). Peptide databases have been built using single nucleotide variants and novel junctions derived from RNA-Seq data that can be used in search engines for sample-specific protein identifications on the same cell lines or tissues. The dasHPPboard has been designed as a tool that can be used to share and visualize a combination of proteomic and transcriptomic data, providing at the same time easy access to resources for proteogenomics analyses. The dasHPPboard can be freely accessed at: http://sphppdashboard.cnb.csic.es.

Proteomic Biomarkers for Spontaneous Preterm Birth

DEFF Research Database (Denmark)

Kacerovsky, Marian; Lenco, Juraj; Musilova, Ivana

2014-01-01

This review aimed to identify, synthesize, and analyze the findings of studies on proteomic biomarkers for spontaneous preterm birth (PTB). Three electronic databases (Medline, Embase, and Scopus) were searched for studies in any language reporting the use of proteomic biomarkers for PTB published...

The epidemiology of Scottish trauma: A comparison of pre-hospital and in-hospital deaths, 2000 to 2011.

Science.gov (United States)

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 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.

External quality assurance for image grading in the Scottish Diabetic Retinopathy Screening Programme.

Science.gov (United States)

Goatman, K A; Philip, S; Fleming, A D; Harvey, R D; Swa, K K; Styles, C; Black, M; Sell, G; Lee, N; Sharp, P F; Olson, J A

2012-06-01

To develop and evaluate an image grading external quality assurance system for the Scottish Diabetic Retinopathy Screening Programme. A web-based image grading system was developed which closely matches the current Scottish national screening software. Two rounds of external quality assurance were run in autumn 2008 and spring 2010, each time using the same 100 images. Graders were compared with a consensus standard derived from the top-level graders' results. After the first round, the centre lead clinicians and top-level graders reviewed the results and drew up guidance notes for the second round. Grader sensitivities ranged from 60.0 to 100% (median 92.5%) in 2008, and from 62.5 to 100% (median 92.5%) in 2010. Specificities ranged from 34.0 to 98.0% (median 86%) in 2008, and 54.0 to 100% (median 88%) in 2010. There was no difference in sensitivity between grader levels, but first-level graders had a significantly lower specificity than level-two and level-three graders. In 2008, one centre had a lower sensitivity but higher specificity than the majority of centres. Following the feedback from the first round, overall agreement improved in 2010 and there were no longer any significant differences between centres. A useful educational tool has been developed for image grading external quality assurance. © 2011 The Authors. Diabetic Medicine © 2011 Diabetes UK.

New structural and functional defects in polyphosphate deficient bacteria: A cellular and proteomic study

Directory of Open Access Journals (Sweden)

Chávez Francisco P

2010-01-01

Full Text Available Abstract Background Inorganic polyphosphate (polyP, a polymer of tens or hundreds of phosphate residues linked by ATP-like bonds, is found in all organisms and performs a wide variety of functions. PolyP is synthesized in bacterial cells by the actions of polyphosphate kinases (PPK1 and PPK2 and degraded by exopolyphosphatase (PPX. Bacterial cells with polyP deficiencies due to knocking out the ppk1 gene are affected in many structural and important cellular functions such as motility, quorum sensing, biofilm formation and virulence among others. The cause of this pleiotropy is not entirely understood. Results The overexpression of exopolyphosphatase in bacteria mimicked some pleitropic defects found in ppk1 mutants. By using this approach we found new structural and functional defects in the polyP-accumulating bacteria Pseudomonas sp. B4, which are most likely due to differences in the polyP-removal strategy. Colony morphology phenotype, lipopolysaccharide (LPS structure changes and cellular division malfunction were observed. Finally, we used comparative proteomics in order to elucidate the cellular adjustments that occurred during polyP deficiency in this bacterium and found some clues that helped to understand the structural and functional defects observed. Conclusions The results obtained suggest that during polyP deficiency energy metabolism and particularly nucleoside triphosphate (NTP formation were affected and that bacterial cells overcame this problem by increasing the flux of energy-generating metabolic pathways such as tricarboxilic acid (TCA cycle, β-oxidation and oxidative phosphorylation and by reducing energy-consuming ones such as active transporters and amino acid biosynthesis. Furthermore, our results suggest that a general stress response also took place in the cell during polyP deficiency.

Proteomic profiling of the epileptic dentate gyrus

OpenAIRE

Li, Aiqing; Choi, Yun-Sik; Dziema, Heather; Cao, Ruifeng; Cho, Hee-Yeon; Jung, Yeon Joo; Obrietan, Karl

2010-01-01

The development of epilepsy is often associated with marked changes in central nervous system cell structure and function. Along these lines, reactive gliosis and granule cell axonal sprouting within the dentate gyrus of the hippocampus are commonly observed in individuals with temporal lobe epilepsy. Here we used the pilocarpine model of temporal lobe epilepsy in mice to screen the proteome and phosphoproteome of the dentate gyrus to identify molecular events that are altered as part of the ...

Proteomic alterations in early stage cervical cancer

OpenAIRE

Güzel, Coşkun; Govorukhina, Natalia; Wisman, G.B.A.; Stingl, Christoph; Dekker, Lennard; Hollema, Harry; Guryev, Victor; Horvatovich, Peter; van der Zee, Ate; Bischoff, Rainer; Luider, Theo

2018-01-01

Laser capture microdissection (LCM) allows the capture of cell types or well-defined structures in tissue. We compared in a semi-quantitative way the proteomes from an equivalent of 8,000 tumor cells from patients with squamous cell cervical cancer (SCC, n = 22) with healthy epithelial and stromal cells obtained from normal cervical tissue (n = 13). Proteins were enzymatically digested into peptides which were measured by high-resolution mass spectrometry and analyzed by “all-or-nothing” anal...

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

Science.gov (United States)

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.

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.

Science.gov (United States)

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), pScottish 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/

Family size and perinatal circumstances, as mental health risk factors in a Scottish birth cohort.

Science.gov (United States)

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.

Relative professional roles in antenatal care: results of a survey in Scottish rural general practice.

Science.gov (United States)

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.

Maternal and neonatal outcomes of antenatal anemia in a Scottish population: a retrospective cohort study.

Science.gov (United States)

Rukuni, Ruramayi; Bhattacharya, Sohinee; Murphy, Michael F; Roberts, David; Stanworth, Simon J; Knight, Marian

2016-05-01

Antenatal anemia is a major public health problem in the UK, yet there is limited high quality evidence for associated poor clinical outcomes. The objectives of this study were to estimate the incidence and clinical outcomes of antenatal anemia in a Scottish population. A retrospective cohort study of 80 422 singleton pregnancies was conducted using data from the Aberdeen Maternal and Neonatal Databank between 1995 and 2012. Antenatal anemia was defined as haemoglobin ≤ 10 g/dl during pregnancy. Incidence was calculated with 95% confidence intervals and compared over time using a chi-squared test for trend. Multivariable logistic regression was used to adjust for confounding variables. Results are presented as adjusted odds ratios with 95% confidence interval. The overall incidence of antenatal anemia was 9.3 cases/100 singleton pregnancies (95% confidence interval 9.1-9.5), decreasing from 16.9/100 to 4.1/100 singleton pregnancies between 1995 and 2012 (p Scottish population. However, given that anemia is a readily correctable risk factor for major causes of morbidity and mortality in the UK, further work is required to investigate appropriate preventive measures. © 2016 Nordic Federation of Societies of Obstetrics and Gynecology.

Extracorporeal membrane oxygenation in a Scottish intensive care unit.

Science.gov (United States)

Berryman, Sean

2010-01-01

I reflected on the training I had on an extraordinary treatment for profound respiratory failure. The result of training enabled us to successfully treat a young female with the influenza A virus with extracorporeal membrane oxygenation (ECMO). I report the positive outcome that occurred, while continuing to run a busy general intensive care unit (ICU). She was the first of six patients who were all successfully treated with ECMO. Ten trained and experienced critical care nurses and two doctors attended the ECMO training course provided by the national centre in the UK. Five patients had already received ECMO therapy in the Scottish specialist unit (over the period of 8 years). As our Scottish specialist unit purchased exactly the same equipment as the national centre, it was easier for the multidisciplinary team to utilize their new-found knowledge and treat future patients with ECMO. With the predicted swine flu (H1N1) pandemic and the subsequent demand for critical care beds, funding was obtained to facilitate ECMO training. The potential need for increased provision of ECMO therapies was highlighted by recent events in Australia and New Zealand. Their most recent winter produced 68 patients requiring ECMO, whereas the previous year had manifested only three. Using our new equipment and adapted protocols from the national centre, we used these new skills to treat our first patient in October 2009. Johns' reflective practice tool was used to evaluate the care provided. Our patient was on ECMO for 9 days. She went on to make a remarkable recovery and was discharged from the ICU 1 week after ECMO was discontinued. She was discharged to the cardiothoracic high-dependency unit, where she was successfully rehabilitated. We were able to successfully treat a young lady, while providing the care for all other patients. This was a complex treatment, one that uses many resources including time and finance. Now that we have all the equipment, the necessary training and the

Proteomics and the Inner Ear

Directory of Open Access Journals (Sweden)

Isolde Thalmann

2001-01-01

Full Text Available The inner ear, one of the most complex organs, contains within its bony shell three sensory systems, the evolutionary oldest gravity receptor system, the three semicircular canals for the detection of angular acceleration, and the auditory system - unrivaled in sensitivity and frequency discrimination. All three systems are susceptible to a host of afflictions affecting the quality of life for all of us. In the first part of this review we present an introduction to the milestones of inner ear research to pave the way for understanding the complexities of a proteomics approach to the ear. Minute sensory structures, surrounded by large fluid spaces and a hard bony shell, pose extreme challenges to the ear researcher. In spite of these obstacles, a powerful preparatory technique was developed, whereby precisely defined microscopic tissue elements can be isolated and analyzed, while maintaining the biochemical state representative of the in vivo conditions. The second part consists of a discussion of proteomics as a tool in the elucidation of basic and pathologic mechanisms, diagnosis of disease, as well as treatment. Examples are the organ of Corti proteins OCP1 and OCP2, oncomodulin, a highly specific calcium-binding protein, and several disease entities, Meniere's disease, benign paroxysmal positional vertigo, and perilymphatic fistula.

[Diet and exercise influence on the proteomic profile of an athlete population].

Science.gov (United States)

Toro, Rocio; Mangas, Alipio; Quezada, Maribel; Rodriguez-Rosety, Manuel; Fournielles, Gabriel; Rodriguez-Rosety, Ignacio; Rodriguez Rosety, Miguel Angel; Alonso, Jose Angel; Garcia-Cozar, Francisco Jose; Duran, Maria Del Carmen

2014-11-01

Nutrition has emerged as a fundamental tool included in the training program of athletes. Body composition seeks different objectives depending on type of sport, position, or time of the season. Furthermore, analysis proteomics allows us to know the structure and function of proteins. To study, using proteomics, the influence of two different diets on the anthropometric profile in a rugby players group. It is a prospective and interventionist study. Thirty-two rugby players were included. Two groups were defined, one followed proteic diet (PD) and, the other group subscribed the Mediterranean diet (MD). All participants were evaluated anthropometrically at the beginning and after six months. A blood sample was taken to twenty -two players, half of each group, used for the proteomic analysis. MD highlight more benefit for these athletes. Two groups were defined based on their anthropometric behavior, G1 and G2. The proteomic analysis related significantly some TGF-family mediators with these groups. MD improves the muscular mass without increasing the total body weight, so this data could be determinant to define profiles for athletes. Some TGF-members could be implicated in the adipose tissue and muscular mass balance. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

OralCard: a bioinformatic tool for the study of oral proteome.

Science.gov (United States)

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.

PCAS – a precomputed proteome annotation database resource

Directory of Open Access Journals (Sweden)

Luo Jingchu

2003-11-01

Full Text Available Abstract Background Many model proteomes or "complete" sets of proteins of given organisms are now publicly available. Much effort has been invested in computational annotation of those "draft" proteomes. Motif or domain based algorithms play a pivotal role in functional classification of proteins. Employing most available computational algorithms, mainly motif or domain recognition algorithms, we set up to develop an online proteome annotation system with integrated proteome annotation data to complement existing resources. Results We report here the development of PCAS (ProteinCentric Annotation System as an online resource of pre-computed proteome annotation data. We applied most available motif or domain databases and their analysis methods, including hmmpfam search of HMMs in Pfam, SMART and TIGRFAM, RPS-PSIBLAST search of PSSMs in CDD, pfscan of PROSITE patterns and profiles, as well as PSI-BLAST search of SUPERFAMILY PSSMs. In addition, signal peptide and TM are predicted using SignalP and TMHMM respectively. We mapped SUPERFAMILY and COGs to InterPro, so the motif or domain databases are integrated through InterPro. PCAS displays table summaries of pre-computed data and a graphical presentation of motifs or domains relative to the protein. As of now, PCAS contains human IPI, mouse IPI, and rat IPI, A. thaliana, C. elegans, D. melanogaster, S. cerevisiae, and S. pombe proteome. PCAS is available at http://pak.cbi.pku.edu.cn/proteome/gca.php Conclusion PCAS gives better annotation coverage for model proteomes by employing a wider collection of available algorithms. Besides presenting the most confident annotation data, PCAS also allows customized query so users can inspect statistically less significant boundary information as well. Therefore, besides providing general annotation information, PCAS could be used as a discovery platform. We plan to update PCAS twice a year. We will upgrade PCAS when new proteome annotation algorithms

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

Science.gov (United States)

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...

Improving HIV proteome annotation: new features of BioAfrica HIV Proteomics Resource.

Science.gov (United States)

Druce, Megan; Hulo, Chantal; Masson, Patrick; Sommer, Paula; Xenarios, Ioannis; Le Mercier, Philippe; De Oliveira, Tulio

2016-01-01

The Human Immunodeficiency Virus (HIV) is one of the pathogens that cause the greatest global concern, with approximately 35 million people currently infected with HIV. Extensive HIV research has been performed, generating a large amount of HIV and host genomic data. However, no effective vaccine that protects the host from HIV infection is available and HIV is still spreading at an alarming rate, despite effective antiretroviral (ARV) treatment. In order to develop effective therapies, we need to expand our knowledge of the interaction between HIV and host proteins. In contrast to virus proteins, which often rapidly evolve drug resistance mutations, the host proteins are essentially invariant within all humans. Thus, if we can identify the host proteins needed for virus replication, such as those involved in transporting viral proteins to the cell surface, we have a chance of interrupting viral replication. There is no proteome resource that summarizes this interaction, making research on this subject a difficult enterprise. In order to fill this gap in knowledge, we curated a resource presents detailed annotation on the interaction between the HIV proteome and host proteins. Our resource was produced in collaboration with ViralZone and used manual curation techniques developed by UniProtKB/Swiss-Prot. Our new website also used previous annotations of the BioAfrica HIV-1 Proteome Resource, which has been accessed by approximately 10 000 unique users a year since its inception in 2005. The novel features include a dedicated new page for each HIV protein, a graphic display of its function and a section on its interaction with host proteins. Our new webpages also add information on the genomic location of each HIV protein and the position of ARV drug resistance mutations. Our improved BioAfrica HIV-1 Proteome Resource fills a gap in the current knowledge of biocuration.Database URL:http://www.bioafrica.net/proteomics/HIVproteome.html. © The Author(s) 2016. Published

Proteomics and the dynamic plasma membrane

DEFF Research Database (Denmark)

Sprenger, Richard R; Jensen, Ole Nørregaard

2010-01-01

plasma membrane is of particular interest, by not only serving as a barrier between the "cell interior" and the external environment, but moreover by organizing and clustering essential components to enable dynamic responses to internal and external stimuli. Defining and characterizing the dynamic plasma...... the challenges in functional proteomic studies of the plasma membrane. We review the recent progress in MS-based plasma membrane proteomics by presenting key examples from eukaryotic systems, including mammals, yeast and plants. We highlight the importance of enrichment and quantification technologies required...... for detailed functional and comparative analysis of the dynamic plasma membrane proteome....

PROTEOMICS in aquaculture: applications and trends.

Science.gov (United States)

Rodrigues, Pedro M; Silva, Tomé S; Dias, Jorge; Jessen, Flemming

2012-07-19

Over the last forty years global aquaculture presented a growth rate of 6.9% per annum with an amazing production of 52.5 million tonnes in 2008, and a contribution of 43% of aquatic animal food for human consumption. In order to meet the world's health requirements of fish protein, a continuous growth in production is still expected for decades to come. Aquaculture is, though, a very competitive market, and a global awareness regarding the use of scientific knowledge and emerging technologies to obtain a better farmed organism through a sustainable production has enhanced the importance of proteomics in seafood biology research. Proteomics, as a powerful comparative tool, has therefore been increasingly used over the last decade to address different questions in aquaculture, regarding welfare, nutrition, health, quality, and safety. In this paper we will give an overview of these biological questions and the role of proteomics in their investigation, outlining the advantages, disadvantages and future challenges. A brief description of the proteomics technical approaches will be presented. Special focus will be on the latest trends related to the aquaculture production of fish with defined nutritional, health or quality properties for functional foods and the integration of proteomics techniques in addressing this challenging issue. Copyright © 2012 Elsevier B.V. All rights reserved.

Proteomics in uveal melanoma.

LENUS (Irish Health Repository)

Ramasamy, Pathma

2014-01-01

Uveal melanoma is the most common primary intraocular malignancy in adults, with an incidence of 5-7 per million per year. It is associated with the development of metastasis in about 50% of cases, and 40% of patients with uveal melanoma die of metastatic disease despite successful treatment of the primary tumour. The survival rates at 5, 10 and 15 years are 65%, 50% and 45% respectively. Unlike progress made in many other areas of cancer, uveal melanoma is still poorly understood and survival rates have remained similar over the past 25 years. Recently, advances made in molecular genetics have improved our understanding of this disease and stratification of patients into low risk and high risk for developing metastasis. However, only a limited number of studies have been performed using proteomic methods. This review will give an overview of various proteomic technologies currently employed in life sciences research, and discuss proteomic studies of uveal melanoma.

CPTAC Collaborates with Molecular & Cellular Proteomics to Address Reproducibility in Targeted Assay Development | Office of Cancer Clinical Proteomics Research

Science.gov (United States)

The journal Molecular & Cellular Proteomics (MCP), in collaboration with the Clinical Proteomic Tumor Analysis Consortium (CPTAC) of the National Cancer Institute (NCI), part of the National Institutes of Health, announce new guidelines and requirements for papers describing the development and application of targeted mass spectrometry measurements of peptides, modified peptides and proteins (Mol Cell Proteomics 2017; PMID: 28183812).  NCI’s participation is part of NIH’s overall effort to address the r

Challenges for proteomics core facilities.

Science.gov (United States)

Lilley, Kathryn S; Deery, Michael J; Gatto, Laurent

2011-03-01

Many analytical techniques have been executed by core facilities established within academic, pharmaceutical and other industrial institutions. The centralization of such facilities ensures a level of expertise and hardware which often cannot be supported by individual laboratories. The establishment of a core facility thus makes the technology available for multiple researchers in the same institution. Often, the services within the core facility are also opened out to researchers from other institutions, frequently with a fee being levied for the service provided. In the 1990s, with the onset of the age of genomics, there was an abundance of DNA analysis facilities, many of which have since disappeared from institutions and are now available through commercial sources. Ten years on, as proteomics was beginning to be utilized by many researchers, this technology found itself an ideal candidate for being placed within a core facility. We discuss what in our view are the daily challenges of proteomics core facilities. We also examine the potential unmet needs of the proteomics core facility that may also be applicable to proteomics laboratories which do not function as core facilities. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An individual urinary proteome analysis in normal human beings to define the minimal sample number to represent the normal urinary proteome

Directory of Open Access Journals (Sweden)

Liu Xuejiao

2012-11-01

Full Text Available Abstract Background The urinary proteome has been widely used for biomarker discovery. A urinary proteome database from normal humans can provide a background for discovery proteomics and candidate proteins/peptides for targeted proteomics. Therefore, it is necessary to define the minimum number of individuals required for sampling to represent the normal urinary proteome. Methods In this study, inter-individual and inter-gender variations of urinary proteome were taken into consideration to achieve a representative database. An individual analysis was performed on overnight urine samples from 20 normal volunteers (10 males and 10 females by 1DLC/MS/MS. To obtain a representative result of each sample, a replicate 1DLCMS/MS analysis was performed. The minimal sample number was estimated by statistical analysis. Results For qualitative analysis, less than 5% of new proteins/peptides were identified in a male/female normal group by adding a new sample when the sample number exceeded nine. In addition, in a normal group, the percentage of newly identified proteins/peptides was less than 5% upon adding a new sample when the sample number reached 10. Furthermore, a statistical analysis indicated that urinary proteomes from normal males and females showed different patterns. For quantitative analysis, the variation of protein abundance was defined by spectrum count and western blotting methods. And then the minimal sample number for quantitative proteomic analysis was identified. Conclusions For qualitative analysis, when considering the inter-individual and inter-gender variations, the minimum sample number is 10 and requires a balanced number of males and females in order to obtain a representative normal human urinary proteome. For quantitative analysis, the minimal sample number is much greater than that for qualitative analysis and depends on the experimental methods used for quantification.

Rebound and disinvestment effects in refined oil consumption and supply resulting from an increase in energy efficiency in the Scottish commercial transport sector

International Nuclear Information System (INIS)

Anson, Sam; Turner, Karen

2009-01-01

In this paper, we use an energy-economy-environment computable general equilibrium (CGE) model of the Scottish economy to examine the impacts of an exogenous increase in energy augmenting technological progress in the domestic commercial Transport sector on the supply and use of energy. We focus our analysis on Scottish refined oil, as the main type of energy input used in commercial transport activity. We find that a 5% increase in energy efficiency in the commercial Transport sector leads to rebound effects in the use of oil-based energy commodities in all time periods, in the target sector and at the economy-wide level. However, our results also suggest that such an efficiency improvement may cause a contraction in capacity in the Scottish refined oil supply sector. This 'disinvestment effect' acts as a constraint on the size of rebound effects. However, the magnitude of rebound effects and presence of the disinvestment effect in the simulations conducted here are sensitive to the specification of key elasticities of substitution in the nested production function for the target sector, particularly the substitutability of energy for non-energy intermediate inputs to production.

Rebound and disinvestment effects in refined oil consumption and supply resulting from an increase in energy efficiency in the Scottish commercial transport sector

Energy Technology Data Exchange (ETDEWEB)

Anson, Sam [Transport Analytical Services, Scottish Government, Victoria Quay, Edinburgh, EH6 6QQ (United Kingdom); Turner, Karen [Department of Economics, University of Strathclyde, Sir William Duncan Building, 130 Rottenrow, Glasgow G4 0GE (United Kingdom)

2009-09-15

In this paper, we use an energy-economy-environment computable general equilibrium (CGE) model of the Scottish economy to examine the impacts of an exogenous increase in energy augmenting technological progress in the domestic commercial Transport sector on the supply and use of energy. We focus our analysis on Scottish refined oil, as the main type of energy input used in commercial transport activity. We find that a 5% increase in energy efficiency in the commercial Transport sector leads to rebound effects in the use of oil-based energy commodities in all time periods, in the target sector and at the economy-wide level. However, our results also suggest that such an efficiency improvement may cause a contraction in capacity in the Scottish refined oil supply sector. This 'disinvestment effect' acts as a constraint on the size of rebound effects. However, the magnitude of rebound effects and presence of the disinvestment effect in the simulations conducted here are sensitive to the specification of key elasticities of substitution in the nested production function for the target sector, particularly the substitutability of energy for non-energy intermediate inputs to production. (author)

Proteomics wants cRacker: automated standardized data analysis of LC-MS derived proteomic data.

Science.gov (United States)

Zauber, Henrik; Schulze, Waltraud X

2012-11-02

The large-scale analysis of thousands of proteins under various experimental conditions or in mutant lines has gained more and more importance in hypothesis-driven scientific research and systems biology in the past years. Quantitative analysis by large scale proteomics using modern mass spectrometry usually results in long lists of peptide ion intensities. The main interest for most researchers, however, is to draw conclusions on the protein level. Postprocessing and combining peptide intensities of a proteomic data set requires expert knowledge, and the often repetitive and standardized manual calculations can be time-consuming. The analysis of complex samples can result in very large data sets (lists with several 1000s to 100,000 entries of different peptides) that cannot easily be analyzed using standard spreadsheet programs. To improve speed and consistency of the data analysis of LC-MS derived proteomic data, we developed cRacker. cRacker is an R-based program for automated downstream proteomic data analysis including data normalization strategies for metabolic labeling and label free quantitation. In addition, cRacker includes basic statistical analysis, such as clustering of data, or ANOVA and t tests for comparison between treatments. Results are presented in editable graphic formats and in list files.

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

Science.gov (United States)

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.

Analysis of biostimulated microbial communities from two field experiments reveals temporal and spatial differences in proteome profiles

Energy Technology Data Exchange (ETDEWEB)

Callister, S.J.; Wilkins, M.J.; Nicora, C.D.; Williams, K.H.; Banfield, J.F.; VerBerkmoes, N.C.; Hettich, R.L.; NGuessan, A.L.; Mouser, P.J.; Elifantz, H.; Smith, R.D.; Lovley, D.R.; Lipton, M.S.; Long, P.E.

2010-07-15

Stimulated by an acetate-amendment field experiment conducted in 2007, anaerobic microbial populations in the aquifer at the Rifle Integrated Field Research Challenge site in Colorado reduced mobile U(VI) to insoluble U(IV). During this experiment, planktonic biomass was sampled at various time points to quantitatively evaluate proteomes. In 2008, an acetate-amended field experiment was again conducted in a similar manner to the 2007 experiment. As there was no comprehensive metagenome sequence available for use in proteomics analysis, we systematically evaluated 12 different organism genome sequences to generate sets of aggregate genomes, or “pseudo-metagenomes”, for supplying relative quantitative peptide and protein identifications. Proteomics results support previous observations of the dominance of Geobacteraceae during biostimulation using acetate as sole electron donor, and revealed a shift from an early stage of iron reduction to a late stage of iron reduction. Additionally, a shift from iron reduction to sulfate reduction was indicated by changes in the contribution of proteome information contributed by different organism genome sequences within the aggregate set. In addition, the comparison of proteome measurements made between the 2007 field experiment and 2008 field experiment revealed differences in proteome profiles. These differences may be the result of alterations in abundance and population structure within the planktonic biomass samples collected for analysis.

Expanding the bovine milk proteome through extensive fractionation

DEFF Research Database (Denmark)

Nissen, Asger; Bendixen, Emøke; Ingvartsen, Klaus Lønne

2013-01-01

Bovine milk is an agricultural product of tremendous value worldwide. It contains proteins, fat, lactose, vitamins, and minerals. It provides nutrition and immunological protection (e.g., in the gastrointestinal tract) to the newborn and young calf. It also forms an important part of human...... of low abundant proteins. Further, the general health and udder health of the dairy cows delivering the milk may influence the composition of the milk proteome. To gain a more exhaustive and true picture of the milk proteome, we performed an extensive preanalysis fractionation of raw composite milk...... nutrition. The repertoire of proteins in milk (i.e., its proteome) is vast and complex. The milk proteome can be described in detail by mass spectrometry-based proteomics. However, the high concentration of dominating proteins in milk reduces mass spectrometry detection sensitivity and limits detection...

Polyphemus, Odysseus and the ovine milk proteome.

Science.gov (United States)

Cunsolo, Vincenzo; Fasoli, Elisa; Di Francesco, Antonella; Saletti, Rosaria; Muccilli, Vera; Gallina, Serafina; Righetti, Pier Giorgio; Foti, Salvatore

2017-01-30

In the last years the amount of ovine milk production, mainly used to formulate a wide range of different and exclusive dairy products often categorized as gourmet food, has been progressively increasing. Taking also into account that sheep milk (SM) also appears to be potentially less allergenic than cow's one, an in-depth information about its protein composition is essential to improve the comprehension of its potential benefits for human consumption. The present work reports the results of an in-depth characterization of SM whey proteome, carried out by coupling the CPLL technology with SDS-PAGE and high resolution UPLC-nESI MS/MS analysis. This approach allowed the identification of 718 different protein components, 644 of which are from unique genes. Particularly, this identification has expanded literature data about sheep whey proteome by 193 novel proteins previously undetected, many of which are involved in the defence/immunity mechanisms or in the nutrient delivery system. A comparative analysis of SM proteome known to date with cow's milk proteome, evidenced that while about 29% of SM proteins are also present in CM, 71% of the identified components appear to be unique of SM proteome and include a heterogeneous group of components which seem to have health-promoting benefits. The data have been deposited to the ProteomeXchange with identifier . Copyright © 2016 Elsevier B.V. All rights reserved.

The Coming Age of Complete, Accurate, and Ubiquitous Proteomes

DEFF Research Database (Denmark)

Mann, M.; Kulak, N.A.; Nagaraj, N.

2013-01-01

High-resolution mass spectrometry (MS)-based proteomics has progressed tremendously over the years. For model organisms like yeast, we can now quantify complete proteomes in just a few hours. Developments discussed in this Perspective will soon enable complete proteome analysis of mammalian cells...

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Seeing beyond statistics: Examining the potential for disjuncture between legislation, policy and practice in meeting the needs of highly able Scottish students

Directory of Open Access Journals (Sweden)

Niamh Stack

2015-03-01

Full Text Available The question of how best to identify and provide for gifted students has a long and contentious history internationally. In contrast to other countries where there are specialist programmes and in some cases specialist teachers for gifted pupils, Scotland has chosen to adopt an inclusive approach to provision for these students and has created a legislative and curricular framework that in theory provides a strong structure for meeting their educational and developmental needs. While there are significant benefits to this approach, care must be taken to ensure that within the space between intention and practice the needs of these learners have been explicitly identified, considered and met. Each year the Scottish Government conducts a census to collect data from all publically funded schools in Scotland. In accordance with Scottish legislation as part of this process it gathers data pertaining to pupils identified as requiring additional support for their learning, including highly able pupils. However there are anomalies within this data, for example, there are unusual and unexplained discrepancies between the proportions of pupils identified as being highly able in different geographical contexts. The purpose of the present study was therefore to examine the potential causes for these anomalies and to assess the implications for the identification of, and provision for, highly able pupils in Scotland. Thirteen structured telephone interviews were conducted with Local Education Authority personnel across Scotland. These interviews aimed to get behind the statistics and examine how highly able pupils are identified, and provided for, in practice. Several interesting issues emerged from the interviews that may begin to help to explain the anomalies and to help us better understand everyday practice. The results, while encouraging, suggest that there is a need for teachers, educational psychologists, schools and authorities to ensure that the

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

Science.gov (United States)

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.

Simple sequence proteins in prokaryotic proteomes

Directory of Open Access Journals (Sweden)

Ramachandran Srinivasan

2006-06-01

Full Text Available Abstract Background The structural and functional features associated with Simple Sequence Proteins (SSPs are non-globularity, disease states, signaling and post-translational modification. SSPs are also an important source of genetic and possibly phenotypic variation. Analysis of 249 prokaryotic proteomes offers a new opportunity to examine the genomic properties of SSPs. Results SSPs are a minority but they grow with proteome size. This relationship is exhibited across species varying in genomic GC, mutational bias, life style, and pathogenicity. Their proportion in each proteome is strongly influenced by genomic base compositional bias. In most species simple duplications is favoured, but in a few cases such as Mycobacteria, large families of duplications occur. Amino acid preference in SSPs exhibits a trend towards low cost of biosynthesis. In SSPs and in non-SSPs, Alanine, Glycine, Leucine, and Valine are abundant in species widely varying in genomic GC whereas Isoleucine and Lysine are rich only in organisms with low genomic GC. Arginine is abundant in SSPs of two species and in the non-SSPs of Xanthomonas oryzae. Asparagine is abundant only in SSPs of low GC species. Aspartic acid is abundant only in the non-SSPs of Halobacterium sp NRC1. The abundance of Serine in SSPs of 62 species extends over a broader range compared to that of non-SSPs. Threonine(T is abundant only in SSPs of a couple of species. SSPs exhibit preferential association with Cell surface, Cell membrane and Transport functions and a negative association with Metabolism. Mesophiles and Thermophiles display similar ranges in the content of SSPs. Conclusion Although SSPs are a minority, the genomic forces of base compositional bias and duplications influence their growth and pattern in each species. The preferences and abundance of amino acids are governed by low biosynthetic cost, evolutionary age and base composition of codons. Abundance of charged amino acids Arginine

Glycoproteins and Glycosylation Site Assignments in Cereal seed Proteomes

DEFF Research Database (Denmark)

Dedvisitsakul, Plaipol

The study of plant proteomes is important to further the understanding of biological processes and enhance the agronomical and nutritional value of crops and food products. To gain deeper understanding on the proteome level, it is important to characterize posttranslational modifications. Glycosy......The study of plant proteomes is important to further the understanding of biological processes and enhance the agronomical and nutritional value of crops and food products. To gain deeper understanding on the proteome level, it is important to characterize posttranslational modifications...

Mathematical biodescriptors of proteomics maps: background and applications.

Science.gov (United States)

Basak, Subhash C; Gute, Brian D

2008-05-01

This article reviews recent developments in the formulation and application of biodescriptors to characterize proteomics maps. Such biodescriptors can be derived by applying techniques from discrete mathematics (graph theory, linear algebra and information theory). This review focuses on the development of biodescriptors for proteomics maps derived from 2D gel electrophoresis. Preliminary results demonstrated that such descriptors have a reasonable ability to differentiate between proteomics patterns that result from exposure to closely related individual chemicals and complex mixtures, such as the jet fuel JP-8. Further research is required to evaluate the utility of these proteomics-based biodescriptors for drug discovery and predictive toxicology.

Characterization of the porcine synovial fluid proteome and a comparison to the plasma proteome

DEFF Research Database (Denmark)

Bennike, Tue Bjerg; Barnaby, Omar; Steen, Hanno

2015-01-01

Synovial fluid is present in all joint cavities, and protects the articular cartilage surfaces in large by lubricating the joint, thus reducing friction. Several studies have described changes in the protein composition of synovial fluid in patients with joint disease. However, the protein concen...... data used in the method optimization, human plasma proteomics data, and search results, have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD000935....

Ethnicity and first birth: age, smoking, delivery, gestation, weight and feeding: Scottish Health and Ethnicity Linkage Study.

Science.gov (United States)

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.

Identification Of Protein Vaccine Candidates Using Comprehensive Proteomic Analysis Strategies

Science.gov (United States)

2007-12-01

that fascinating fungus known as Coccidioides. I also want to thank the UA Mass Spectrometry Facility and the UA Proteomics Consortium, especially...W. & N. N. Kav. 2006. The proteome of the phytopathogenic fungus Sclerotinia sclerotiorum. Proteomics 6: 5995-6007. 127. de Godoy, L. M., J. V...IDENTIFICATION OF PROTEIN VACCINE CANDIDATES USING COMPREHENSIVE PROTEOMIC ANALYSIS STRATEGIES by James G. Rohrbough

Serum proteome profiling in canine idiopathic dilated cardiomyopathy using TMT-based quantitative proteomics approach.

Science.gov (United States)

Bilić, Petra; Guillemin, Nicolas; Kovačević, Alan; Beer Ljubić, Blanka; Jović, Ines; Galan, Asier; Eckersall, Peter David; Burchmore, Richard; Mrljak, Vladimir

2018-05-15

Idiopathic dilated cardiomyopathy (iDCM) is a primary myocardial disorder with an unknown aetiology, characterized by reduced contractility and ventricular dilation of the left or both ventricles. Naturally occurring canine iDCM was used herein to identify serum proteomic signature of the disease compared to the healthy state, providing an insight into underlying mechanisms and revealing proteins with biomarker potential. To achieve this, we used high-throughput label-based quantitative LC-MS/MS proteomics approach and bioinformatics analysis of the in silico inferred interactome protein network created from the initial list of differential proteins. To complement the proteomic analysis, serum biochemical parameters and levels of know biomarkers of cardiac function were measured. Several proteins with biomarker potential were identified, such as inter-alpha-trypsin inhibitor heavy chain H4, microfibril-associated glycoprotein 4 and apolipoprotein A-IV, which were validated using an independent method (Western blotting) and showed high specificity and sensitivity according to the receiver operating characteristic curve analysis. Bioinformatics analysis revealed involvement of different pathways in iDCM, such as complement cascade activation, lipoprotein particles dynamics, elastic fibre formation, GPCR signalling and respiratory electron transport chain. Idiopathic dilated cardiomyopathy is a severe primary myocardial disease of unknown cause, affecting both humans and dogs. This study is a contribution to the canine heart disease research by means of proteomic and bioinformatic state of the art analyses, following similar approach in human iDCM research. Importantly, we used serum as non-invasive and easily accessible biological source of information and contributed to the scarce data on biofluid proteome research on this topic. Bioinformatics analysis revealed biological pathways modulated in canine iDCM with potential of further targeted research. Also, several

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

Science.gov (United States)

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…

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

Science.gov (United States)

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…

Birth weight and cognitive function at age 11 years: the Scottish Mental Survey 1932

OpenAIRE

Shenkin, S; Starr, J; Pattie, A; Rush, M; Whalley, L; Deary, I; PHARAOH, E. P.

2001-01-01

AIMS—To examine the relation between birth weight and cognitive function at age 11 years, and to examine whether this relation is independent of social class.
METHODS—Retrospective cohort study based on birth records from 1921 and cognitive function measured while at school at age 11 in 1932.Subjects were 985 live singletons born in the Edinburgh Royal Maternity and Simpson Memorial Hospital in 1921. Moray House Test scores from the Scottish Mental Survey 1932 were trace...

Polybrominated diphenyl ethers do not affect metamorphosis but alter the proteome of the invasive slipper limpet Crepidula onyx.

Science.gov (United States)

Mukherjee, Joy; Po, Beverly H K; Chiu, Jill M Y; Wu, Rudolf S S; Qian, Pei-Yuan; Thiyagarajan, Vengatesen

2013-08-15

Man-made polybrominated diphenyl ethers (PBDEs) used as flame retardants in various consumer products may be harmful to marine organisms. Larvae of some marine invertebrates, especially invasive species, can develop resistance to PBDEs through altered protein expression patterns or proteome plasticity. This is the first report of a proteomics approach to study BDE-47 induced molecular changes in the invasive limpet Crepidula onyx. Larvae of C. onyx were cultured for 5 days (hatching to metamorphosis) in the presence of BDE-47 (1 μg L(-1)). Using a 2-DE proteomics approach with triple quadrupole and high-resolution TOF-MS, we showed that BDE-47 altered the proteome structure but not the growth or metamorphosis of C. onyx larvae. We found eight significant differentially expressed proteins in response to BDE-47, deemed the protein expression signature, consisting of cytoskeletal, stress tolerance, metabolism and energy production related proteins. Our data suggest C. onyx larvae have adequate proteome plasticity to tolerate BDE-47 toxicity. Copyright © 2013 Elsevier Ltd. All rights reserved.

Proteomics: Protein Identification Using Online Databases

Science.gov (United States)

Eurich, Chris; Fields, Peter A.; Rice, Elizabeth

2012-01-01

Proteomics is an emerging area of systems biology that allows simultaneous study of thousands of proteins expressed in cells, tissues, or whole organisms. We have developed this activity to enable high school or college students to explore proteomic databases using mass spectrometry data files generated from yeast proteins in a college laboratory…

Modification-specific proteomics in plant biology

DEFF Research Database (Denmark)

Ytterberg, A Jimmy; Jensen, Ole N

2010-01-01

and proteomics. In general, methods for PTM characterization are developed to study yeast and mammalian biology and later adopted to investigate plants. Our point of view is that it is advantageous to enrich for PTMs on the peptide level as part of a quantitative proteomics strategy to not only identify the PTM...

Aspiration, Agency, and the Production of New Selves in a Scottish New Town, c.1947-c.2016.

Science.gov (United States)

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.

Identification of Cryptosporidium Species and Genotypes in Scottish Raw and Drinking Waters during a One-Year Monitoring Period▿

Science.gov (United States)

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

Correlations of indoor second-hand smoking, household smoking rules, regional deprivation and children mental health: Scottish Health Survey, 2013.

Science.gov (United States)

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 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.

Improving Outcomes through Transformational Health and Social Care Integration - The Scottish Experience.

Science.gov (United States)

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.

Biomarker discovery in mass spectrometry-based urinary proteomics.

Science.gov (United States)

Thomas, Samuel; Hao, Ling; Ricke, William A; Li, Lingjun

2016-04-01

Urinary proteomics has become one of the most attractive topics in disease biomarker discovery. MS-based proteomic analysis has advanced continuously and emerged as a prominent tool in the field of clinical bioanalysis. However, only few protein biomarkers have made their way to validation and clinical practice. Biomarker discovery is challenged by many clinical and analytical factors including, but not limited to, the complexity of urine and the wide dynamic range of endogenous proteins in the sample. This article highlights promising technologies and strategies in the MS-based biomarker discovery process, including study design, sample preparation, protein quantification, instrumental platforms, and bioinformatics. Different proteomics approaches are discussed, and progresses in maximizing urinary proteome coverage and standardization are emphasized in this review. MS-based urinary proteomics has great potential in the development of noninvasive diagnostic assays in the future, which will require collaborative efforts between analytical scientists, systems biologists, and clinicians. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Plant Abiotic Stress Proteomics: The Major Factors Determining Alterations in Cellular Proteome

Science.gov (United States)

Kosová, Klára; Vítámvás, Pavel; Urban, Milan O.; Prášil, Ilja T.; Renaut, Jenny

2018-01-01

HIGHLIGHTS: Major environmental and genetic factors determining stress-related protein abundance are discussed.Major aspects of protein biological function including protein isoforms and PTMs, cellular localization and protein interactions are discussed.Functional diversity of protein isoforms and PTMs is discussed. Abiotic stresses reveal profound impacts on plant proteomes including alterations in protein relative abundance, cellular localization, post-transcriptional and post-translational modifications (PTMs), protein interactions with other protein partners, and, finally, protein biological functions. The main aim of the present review is to discuss the major factors determining stress-related protein accumulation and their final biological functions. A dynamics of stress response including stress acclimation to altered ambient conditions and recovery after the stress treatment is discussed. The results of proteomic studies aimed at a comparison of stress response in plant genotypes differing in stress adaptability reveal constitutively enhanced levels of several stress-related proteins (protective proteins, chaperones, ROS scavenging- and detoxification-related enzymes) in the tolerant genotypes with respect to the susceptible ones. Tolerant genotypes can efficiently adjust energy metabolism to enhanced needs during stress acclimation. Stress tolerance vs. stress susceptibility are relative terms which can reflect different stress-coping strategies depending on the given stress treatment. The role of differential protein isoforms and PTMs with respect to their biological functions in different physiological constraints (cellular compartments and interacting partners) is discussed. The importance of protein functional studies following high-throughput proteome analyses is presented in a broader context of plant biology. In summary, the manuscript tries to provide an overview of the major factors which have to be considered when interpreting data from proteomic

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

Science.gov (United States)

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…

Data in support of metabolic reprogramming in transformed mouse cortical astrocytes: A proteomic study

Directory of Open Access Journals (Sweden)

Azeddine Bentaib

2015-03-01

Full Text Available 2D-DIGE analysis coupled with mass spectrometry is a global, without a priori, comparative proteomic approach particularly suited to identify and quantify enzymes isoforms and structural proteins, thus making it an efficient tool for the characterization of the changes in cell phenotypes that occur in physiological and pathological conditions. In this data article in support of the research article entitled “Metabolic reprogramming in transformed mouse cortical astrocytes: a proteomic study” [1] we illustrate the changes in protein profile that occur during the metabolic reprogramming undergone by cultured mouse astrocytes in a model of in-vitro cancerous transformation [2].

Proteomic approaches in cancer risk and response assessment.

Science.gov (United States)

Petricoin, Emanuel F; Liotta, Lance A

2004-02-01

Proteomics is more than just a list-generating exercise where increases or decreases in protein expression are identified. Proteomic technologies will ultimately characterize information-flow through the protein circuitry that interconnects the extracellular microenvironment to the serum or plasma macroenvironment through intracellular signaling systems and their control of gene transcription. The nature of this information can be a cause or a consequence of disease processes and how patients respond to therapy. Analysis of human cancer as a model for how proteomics can have an impact at the bedside can take advantage of several promising new proteomic technologies. These technologies are being developed for early detection and risk assessment, therapeutic targeting and patient-tailored therapy.

Proteomic approach to nanotoxicity.

Science.gov (United States)

Matysiak, Magdalena; Kapka-Skrzypczak, Lucyna; Brzóska, Kamil; Gutleb, Arno C; Kruszewski, Marcin

2016-03-30

In recent years a large number of engineered nanomaterials (NMs) have been developed with promising technical benefits for consumers and medical appliances. In addition to already known potentially advantageous biological properties (antibiotic, antifungal and antiviral activity) of NMs, many new medical applications of NMs are foreseen, such as drug carriers, contrast agents, radiopharmaceuticals and many others. However, there is increasing concern about potential environmental and health effects due to NMs exposure. An increasing body of evidence suggests that NMs may trigger undesirable hazardous interactions with biological systems with potential to generate harmful effects. In this review we summarized a current state of knowledge on the proteomics approaches to nanotoxicity, including protein corona formation, in vitro and in vivo effects of exposure to NMs on proteome of different classes of organisms, from bacteria and plants to mammals. The effects of NMs on the proteome of environmentally relevant organisms are also described. Despite the benefit that development of nanotechnology may bring to the society, there are still major gaps of knowledge on the influence of nanomaterials on human health and the environment. Thus, it seems necessary to conduct further interdisciplinary research to fill the knowledge gaps in NM toxicity, using more holistic approaches than offered by conventional biological techniques. “OMICS” techniques will certainly help researchers in this field. In this paper we summarized the current stage of knowledge of the effects of nanoparticles on the proteome of different organisms, including those commonly used as an environmentally relevant indicator organisms.

A structured proteomic approach identifies 14-3-3Sigma as a novel and reliable protein biomarker in panel based differential diagnostics of liver tumors.

Science.gov (United States)

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.

Activity of Scottish plant, lichen and fungal endophyte extracts against Mycobacterium aurum and Mycobacterium tuberculosis.

Science.gov (United States)

Gordien, Andréa Y; Gray, Alexander I; Ingleby, Kevin; Franzblau, Scott G; Seidel, Véronique

2010-05-01

With tuberculosis the leading bacterial killer worldwide and other mycobacterial diseases on the increase, the search for new antimycobacterial agents is timely. In this study, extracts from plants, lichens and fungal endophytes of Scottish provenance were screened for activity against Mycobacterium aurum and M. tuberculosis H(37)Rv. The best activity against M. aurum was observed for extracts of Juniperus communis roots and Cladonia arbuscula (MIC = 4 microg/mL), and a fungal endophyte isolated from Vaccinium myrtillus (MIC = 8 microg/mL). The best activity against M. tuberculosis was observed for extracts of C. arbuscula, Empetrum nigrum, J. communis roots, Calluna vulgaris aerial parts, Myrica gale roots and stems (93 to 99% inhibition at 100 microg/mL). Potent antitubercular activity (90 to 96% inhibition at 100 microg/mL) was also observed for the ethanol extracts of Xerocomus badius, Chalciporus piperatus, Suillus luteus and of endophytes isolated from C. vulgaris, E. nigrum, Vaccinium vitis-idaea and V. myrtillus. The results obtained this study provide, in part, some scientific basis for the traditional use of some of the selected plants in the treatment of tuberculosis. They also indicate that fungal endophytes recovered from Scottish plants are a source of antimycobacterial agents worthy of further investigation. Copyright (c) 2009 John Wiley & Sons, Ltd.

The quest of the human proteome and the missing proteins: digging deeper.

Science.gov (United States)

Reddy, Panga Jaipal; Ray, Sandipan; Srivastava, Sanjeeva

2015-05-01

Given the diverse range of transcriptional and post-transcriptional mechanisms of gene regulation, the estimates of the human proteome is likely subject to scientific surprises as the field of proteomics has gained momentum worldwide. In this regard, the establishment of the "Human Proteome Draft" using high-resolution mass spectrometry (MS), tissue microarrays, and immunohistochemistry by three independent research groups (laboratories of Pandey, Kuster, and Uhlen) accelerated the pace of proteomics research. The Chromosome Centric Human Proteome Project (C-HPP) has taken initiative towards the completion of the Human Proteome Project (HPP) so as to understand the proteomics correlates of common complex human diseases and biological diversity, not to mention person-to-person and population differences in response to drugs, nutrition, vaccines, and other health interventions and host-environment interactions. Although high-resolution MS-based and antibody microarray approaches have shown enormous promises, we are still unable to map the whole human proteome due to the presence of numerous "missing proteins." In December 2014, at the Indian Institute of Technology Bombay, Mumbai the 6(th) Annual Meeting of the Proteomics Society, India (PSI) and the International Proteomics Conference was held. As part of this interdisciplinary summit, a panel discussion session on "The Quest of the Human Proteome and Missing Proteins" was organized. Eminent scientists in the field of proteomics and systems biology, including Akhilesh Pandey, Gilbert S. Omenn, Mark S. Baker, and Robert L. Mortiz, shed light on different aspects of the human proteome drafts and missing proteins. Importantly, the possible reasons for the "missing proteins" in shotgun MS workflow were identified and debated by experts as low tissue expression, lack of enzymatic digestion site, or protein lost during extraction, among other contributing factors. To capture the missing proteins, the experts' collective

A community proposal to integrate proteomics activities in ELIXIR.

Science.gov (United States)

Vizcaíno, Juan Antonio; Walzer, Mathias; Jiménez, Rafael C; Bittremieux, Wout; Bouyssié, David; Carapito, Christine; Corrales, Fernando; Ferro, Myriam; Heck, Albert J R; Horvatovich, Peter; Hubalek, Martin; Lane, Lydie; Laukens, Kris; Levander, Fredrik; Lisacek, Frederique; Novak, Petr; Palmblad, Magnus; Piovesan, Damiano; Pühler, Alfred; Schwämmle, Veit; Valkenborg, Dirk; van Rijswijk, Merlijn; Vondrasek, Jiri; Eisenacher, Martin; Martens, Lennart; Kohlbacher, Oliver

2017-01-01

Computational approaches have been major drivers behind the progress of proteomics in recent years. The aim of this white paper is to provide a framework for integrating computational proteomics into ELIXIR in the near future, and thus to broaden the portfolio of omics technologies supported by this European distributed infrastructure. This white paper is the direct result of a strategy meeting on 'The Future of Proteomics in ELIXIR' that took place in March 2017 in Tübingen (Germany), and involved representatives of eleven ELIXIR nodes. These discussions led to a list of priority areas in computational proteomics that would complement existing activities and close gaps in the portfolio of tools and services offered by ELIXIR so far. We provide some suggestions on how these activities could be integrated into ELIXIR's existing platforms, and how it could lead to a new ELIXIR use case in proteomics. We also highlight connections to the related field of metabolomics, where similar activities are ongoing. This white paper could thus serve as a starting point for the integration of computational proteomics into ELIXIR. Over the next few months we will be working closely with all stakeholders involved, and in particular with other representatives of the proteomics community, to further refine this paper.

"Does understanding the brain need proteomics and does understanding proteomics need brains?"--Second HUPO HBPP Workshop hosted in Paris.

Science.gov (United States)

Hamacher, Michael; Klose, Joachim; Rossier, Jean; Marcus, Katrin; Meyer, Helmut E

2004-07-01

The second Human Brain Proteome Project (HBPP) Workshop of the Human Proteome Organisation (HUPO) took place at the Ecole Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI) from April 23-24, 2004. During two days, more than 70 attendees from Europe, Asia and the US came together to decide basic strategic approaches, standards and the beginning of a pilot phase prior to further studies of the human brain proteome. The international consortium presented the technological and scientific portfolio and scheduled the time table for the next year.

Proteomic analysis of cell walls of two developmental stages of alfalfa stems

Directory of Open Access Journals (Sweden)

Julian C Verdonk

2012-12-01

Full Text Available Cell walls are important for the growth and development of all plants. They are also valuable resources for feed and fiber, and more recently as a potential feedstock for bioenergy production. Cell wall proteins comprise only a fraction of the cell wall, but play important roles in establishing the walls and in the chemical interactions (e.g. crosslinking of cell wall components. This crosslinking provides structure, but restricts digestibility of cell wall complex carbohydrates, limiting available energy in animal and bioenergy production systems. Manipulation of cell wall proteins could be a strategy to improve digestibility. An analysis of the cell wall proteome of apical alfalfa stems (less mature, more digestible and basal alfalfa stems (more mature, less digestible was conducted using a recently developed low-salt/density gradient method for the isolation of cell walls. Walls were subsequently subjected to a modified extraction utilizing EGTA to remove pectins, followed by a LiCl extraction to isolate more tightly bound proteins. Recovered proteins were identified using shotgun proteomics. We identified 272 proteins in the alfalfa stem cell wall proteome, 153 of which had not previously been identified in cell wall proteomic analyses. Nearly 70% percent of the identified proteins were predicted to be secreted, as would be expected for most cell wall proteins, an improvement over previously published studies using traditional cell wall isolation methods. A comparison of our and several other cell wall proteomic studies indicates little overlap in identified proteins among them, which may be largely due to differences in the tissues used as well as differences in experimental approach.

The proteome of neurofilament-containing protein aggregates in blood

Directory of Open Access Journals (Sweden)

Rocco Adiutori

2018-07-01

Full Text Available Protein aggregation in biofluids is a poorly understood phenomenon. Under normal physiological conditions, fluid-borne aggregates may contain plasma or cell proteins prone to aggregation. Recent observations suggest that neurofilaments (Nf, the building blocks of neurons and a biomarker of neurodegeneration, are included in high molecular weight complexes in circulation. The composition of these Nf-containing hetero-aggregates (NCH may change in systemic or organ-specific pathologies, providing the basis to develop novel disease biomarkers. We have tested ultracentrifugation (UC and a commercially available protein aggregate binder, Seprion PAD-Beads (SEP, for the enrichment of NCH from plasma of healthy individuals, and then characterised the Nf content of the aggregate fractions using gel electrophoresis and their proteome by mass spectrometry (MS. Western blot analysis of fractions obtained by UC showed that among Nf isoforms, neurofilament heavy chain (NfH was found within SDS-stable high molecular weight aggregates. Shotgun proteomics of aggregates obtained with both extraction techniques identified mostly cell structural and to a lesser extent extra-cellular matrix proteins, while functional analysis revealed pathways involved in inflammatory response, phagosome and prion-like protein behaviour. UC aggregates were specifically enriched with proteins involved in endocrine, metabolic and cell-signalling regulation. We describe the proteome of neurofilament-containing aggregates isolated from healthy individuals biofluids using different extraction methods.

Birth weight and cognitive function at age 11years: the Scottish Mental Survey 1932

OpenAIRE

Shenkin, S D; Starr, John M; Pattie, Alison; Rush, M A; Whalley, Lawrence J; Deary, Ian J

2001-01-01

AIMS---To examine the relation between birth weight and cognitive function at age 11 years, and to examine whether this relation is independent of social class. METHODS---Retrospective cohort study based on birth records from 1921 and cognitive function measured while at school at age 11 in 1932. Subjects were 985 live singletons born in the Edinburgh Royal Maternity and Simpson Memorial Hospital in 1921. Moray House Test scores from the Scottish Mental Survey 1932 were traced on 449 of th...

Pre-fractionation strategies to resolve pea (Pisum sativum sub-proteomes

Directory of Open Access Journals (Sweden)

Claudia Nicole Meisrimler

2015-10-01

Full Text Available Legumes are important crop plants and pea (Pisum sativum L. has been investigated as a model with respect to several physiological aspects. The sequencing of the pea genome has not been completed. Therefore, proteomic approaches are currently limited. Nevertheless, the increasing numbers of available EST-databases as well as the high homology of the pea and medicago genome (Medicago truncatula G. allow the successful identification of proteins. Due to the un-sequenced pea genome, pre-fractionation approaches have been used in pea proteomic surveys in the past. Aside from a number of selective proteome studies on crude extracts and the chloroplast, few studies have targeted other components such as the pea secretome, an important sub-proteome of interest due to its role in abiotic and biotic stress processes. The secretome itself can be further divided into different sub-proteomes (plasma membrane, apoplast, cell wall proteins. Cell fractionation in combination with different gel-electrophoresis, chromatography methods and protein identification by mass spectrometry are important partners to gain insight into pea sub-proteomes, post-translational modifications and protein functions. Overall, pea proteomics needs to link numerous existing physiological and biochemical data to gain further insight into adaptation processes, which play important roles in field applications. Future developments and directions in pea proteomics are discussed.

Proteomic and metabolomic approaches to biomarker discovery

CERN Document Server

Issaq, Haleem J

2013-01-01

Proteomic and Metabolomic Approaches to Biomarker Discovery demonstrates how to leverage biomarkers to improve accuracy and reduce errors in research. Disease biomarker discovery is one of the most vibrant and important areas of research today, as the identification of reliable biomarkers has an enormous impact on disease diagnosis, selection of treatment regimens, and therapeutic monitoring. Various techniques are used in the biomarker discovery process, including techniques used in proteomics, the study of the proteins that make up an organism, and metabolomics, the study of chemical fingerprints created from cellular processes. Proteomic and Metabolomic Approaches to Biomarker Discovery is the only publication that covers techniques from both proteomics and metabolomics and includes all steps involved in biomarker discovery, from study design to study execution.  The book describes methods, and presents a standard operating procedure for sample selection, preparation, and storage, as well as data analysis...

Characterization of individual mouse cerebrospinal fluid proteomes

Energy Technology Data Exchange (ETDEWEB)

Smith, Jeffrey S.; Angel, Thomas E.; Chavkin, Charles; Orton, Daniel J.; Moore, Ronald J.; Smith, Richard D.

2014-03-20

Analysis of cerebrospinal fluid (CSF) offers key insight into the status of the central nervous system. Characterization of murine CSF proteomes can provide a valuable resource for studying central nervous system injury and disease in animal models. However, the small volume of CSF in mice has thus far limited individual mouse proteome characterization. Through non-terminal CSF extractions in C57Bl/6 mice and high-resolution liquid chromatography-mass spectrometry analysis of individual murine samples, we report the most comprehensive proteome characterization of individual murine CSF to date. Utilizing stringent protein inclusion criteria that required the identification of at least two unique peptides (1% false discovery rate at the peptide level) we identified a total of 566 unique proteins, including 128 proteins from three individual CSF samples that have been previously identified in brain tissue. Our methods and analysis provide a mechanism for individual murine CSF proteome analysis.

“Weary for the Heather and the Deer”: R. L. Stevenson Depicts the Scottish Diasporic Experience

Directory of Open Access Journals (Sweden)

Christy Danelle Di Frances

2015-07-01

Full Text Available Robert Louis Stevenson is well known as a writer of popular Victorian adventures, yet much of his fiction is steeped in the cultural and historical preoccupations of Scotland. Texts such as Kidnapped (1886, The Master of Ballantrae (1889, and Catriona (1893 hinge upon culturally significant events such as the Jacobite Rising of 1745 and the Appin Murder. These works also allude to the Highland Clearances of the eighteenth and nineteenth centuries and the Battle of Culloden with its ensuing disarming acts—all occurrences which contributed to or comprised significant catalysts for the large-scale expulsion of Scots from their homeland. Certainly, themes of exile pervade Stevenson’s Scottish work and maintain a more liminal presence in his later South Seas fiction, and many of the author’s finest characters can be read as enactments of temporary or permanent expatriates whose real-life counterparts form a fascinating cross-section of the diasporic movement. This paper focuses on several of these characters, whose adventures are encoded into their corresponding texts as fictional re-constructions of a broader experience common to displaced Scots in the eighteenth and nineteenth centuries. Some are driven from Scotland as a direct result of economic hardship or domestic conflict, while others leave (at least temporarily as a means of avoiding the political corruption and intrigue characteristic of the historical struggle for Scottish independence. Through characters like David Balfour, Alan Breck Stewart, James Durie, and Archie Weir, Stevenson explores the psychological ramifications of politically enforced and self-imposed exile, thus providing fictional extrapolations of the Scottish diasporic experience. These portrayals, infused with a the author’s own experiences abroad, offer fascinating microcosms which gesture towards the collective experience of a wide-scale network of displaced Scots in the Victorian world. An early version of this

Proteomic profiling of Bifidobacterium bifidum S17 cultivated under in vitro conditions

Directory of Open Access Journals (Sweden)

Xiao eWei

2016-02-01

Full Text Available Bifidobacteria are frequently used in probiotic food and dairy products. Bifidobacterium bifidum S17 is a promising probiotic candidate strain that displays strong adhesion to intestinal epithelial cells and elicits potent anti-inflammatory capacity both in vitro and in murine models of colitis. The recently sequenced genome of B. bifidum S17 has a size of about 2.2 Mb and encodes 1,782 predicted protein-coding genes. In the present study, a comprehensive proteomic profiling was carried out to identify and characterize proteins expressed by B. bifidum S17. A total of 1148 proteins entries were identified by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS, representing 64.4% of the predicted proteome. 719 proteins could be assigned to functional categories according to cluster of orthologous groups of proteins (COGs. The COG distribution of the detected proteins highly correlates with that of the complete predicted proteome suggesting a good coverage and representation of the genomic content of B. bifidum S17 by the proteome. COGs that were highly present in the proteome of B. bifidum S17 were Translation, Amino Acid Transport and Metabolism, and Carbohydrate Transport and Metabolism. Complete sets of enzymes for both the bifidus shunt and the Embden-Meyerhof pathway were identified. Further bioinformatic analysis yielded 28 proteins with a predicted extracellular localization including 14 proteins with an LPxTG-motif for cell wall anchoring and two proteins (elongation factor Tu and enolase with a potential moonlighting function in adhesion. Amongst the predicted extracellular proteins were five of six pilin proteins encoded in the B. bifidum S17 genome as well as several other proteins with a potential role in interaction with host structures. The presented results are the first compilation of a proteomic reference profile for a B. bifidum strain and will facilitate analysis of the molecular mechanisms of physiology, host

Community and Proteomic Analysis of Anaerobic Consortia Converting Tetramethylammonium to Methane

Directory of Open Access Journals (Sweden)

Wei-Yu Chen

2017-01-01

Full Text Available Tetramethylammonium-degrading methanogenic consortia from a complete-mixing suspended sludge (CMSS and an upflow anaerobic sludge blanket (UASB reactors were studied using multiple PCR-based molecular techniques and shotgun proteomic approach. The prokaryotic 16S rRNA genes of the consortia were analyzed by quantitative PCR, high-throughput sequencing, and DGGE-cloning methods. The results showed that methanogenic archaea were highly predominant in both reactors but differed markedly according to community structure. Community and proteomic analysis revealed that Methanomethylovorans and Methanosarcina were the major players for the demethylation of methylated substrates and methane formation through the reduction pathway of methyl-S-CoM and possibly, acetyl-CoA synthase/decarbonylase-related pathways. Unlike high dominance of one Methanomethylovorans population in the CMSS reactor, diverse methylotrophic Methanosarcina species inhabited in syntrophy-like association with hydrogenotrophic Methanobacterium in the granular sludge of UASB reactor. The overall findings indicated the reactor-dependent community structures of quaternary amines degradation and provided microbial insight for the improved understanding of engineering application.

Community and Proteomic Analysis of Anaerobic Consortia Converting Tetramethylammonium to Methane

Science.gov (United States)

Chen, Wei-Yu; Kraková, Lucia; Pangallo, Domenico; Jeszeová, Lenka; Liu, Bing; Yasui, Hidenari

2017-01-01

Tetramethylammonium-degrading methanogenic consortia from a complete-mixing suspended sludge (CMSS) and an upflow anaerobic sludge blanket (UASB) reactors were studied using multiple PCR-based molecular techniques and shotgun proteomic approach. The prokaryotic 16S rRNA genes of the consortia were analyzed by quantitative PCR, high-throughput sequencing, and DGGE-cloning methods. The results showed that methanogenic archaea were highly predominant in both reactors but differed markedly according to community structure. Community and proteomic analysis revealed that Methanomethylovorans and Methanosarcina were the major players for the demethylation of methylated substrates and methane formation through the reduction pathway of methyl-S-CoM and possibly, acetyl-CoA synthase/decarbonylase-related pathways. Unlike high dominance of one Methanomethylovorans population in the CMSS reactor, diverse methylotrophic Methanosarcina species inhabited in syntrophy-like association with hydrogenotrophic Methanobacterium in the granular sludge of UASB reactor. The overall findings indicated the reactor-dependent community structures of quaternary amines degradation and provided microbial insight for the improved understanding of engineering application. PMID:29391857

Inspection, visualisation and analysis of quantitative proteomics data

OpenAIRE

Gatto, Laurent

2016-01-01

Material Quantitative Proteomics and Data Analysis Course. 4 - 5 April 2016, Queen Hotel, Chester, UK Table D - Inspection, visualisation and analysis of quantitative proteomics data, Laurent Gatto (University of Cambridge)

Revisiting biomarker discovery by plasma proteomics

DEFF Research Database (Denmark)

Geyer, Philipp E; Holdt, Lesca M; Teupser, Daniel

2017-01-01

slow rate. As described in this review, mass spectrometry (MS)-based proteomics has become a powerful technology in biological research and it is now poised to allow the characterization of the plasma proteome in great depth. Previous "triangular strategies" aimed at discovering single biomarker...

Expanding the bovine milk proteome through extensive fractionation.

Science.gov (United States)

Nissen, Asger; Bendixen, Emøke; Ingvartsen, Klaus Lønne; Røntved, Christine Maria

2013-01-01

Bovine milk is an agricultural product of tremendous value worldwide. It contains proteins, fat, lactose, vitamins, and minerals. It provides nutrition and immunological protection (e.g., in the gastrointestinal tract) to the newborn and young calf. It also forms an important part of human nutrition. The repertoire of proteins in milk (i.e., its proteome) is vast and complex. The milk proteome can be described in detail by mass spectrometry-based proteomics. However, the high concentration of dominating proteins in milk reduces mass spectrometry detection sensitivity and limits detection of low abundant proteins. Further, the general health and udder health of the dairy cows delivering the milk may influence the composition of the milk proteome. To gain a more exhaustive and true picture of the milk proteome, we performed an extensive preanalysis fractionation of raw composite milk collected from documented healthy cows in early lactation. Four simple and industrially applicable techniques exploring the physical and chemical properties of milk, including acidification, filtration, and centrifugation, were used for separation of the proteins. This resulted in 5 different fractions, whose content of proteins were compared with the proteins of nonfractionated milk using 2-dimensional liquid chromatography tandem mass spectrometry analysis. To validate the proteome analysis, spectral counts and ELISA were performed on 7 proteins using the ELISA for estimation of the detection sensitivity limit of the 2-dimensional liquid chromatography tandem mass spectrometry analysis. Each fractionation technique resulted in identification of a unique subset of proteins. However, high-speed centrifugation of milk to whey was by far the best method to achieve high and repeatable proteome coverage. The total number of milk proteins initially detected in nonfractionated milk and the fractions were 635 in 2 replicates. Removal of dominant proteins and filtering for redundancy across the

Comprehensive proteomic analysis of human pancreatic juice

DEFF Research Database (Denmark)

Grønborg, Mads; Bunkenborg, Jakob; Kristiansen, Troels Zakarias

2004-01-01

Proteomic technologies provide an excellent means for analysis of body fluids for cataloging protein constituents and identifying biomarkers for early detection of cancers. The biomarkers currently available for pancreatic cancer, such as CA19-9, lack adequate sensitivity and specificity...... contributing to late diagnosis of this deadly disease. In this study, we carried out a comprehensive characterization of the "pancreatic juice proteome" in patients with pancreatic adenocarcinoma. Pancreatic juice was first fractionated by 1-dimensional gel electrophoresis and subsequently analyzed by liquid...... in this study could be directly assessed for their potential as biomarkers for pancreatic cancer by quantitative proteomics methods or immunoassays....

Proteomic characterization of golgi membranes enriched from Arabidopsis suspension cell cultures

DEFF Research Database (Denmark)

Hansen, Sara Fasmer; Ebert, Berit; Rautengarten, Carsten

2016-01-01

The plant Golgi apparatus has a central role in the secretory pathway and is the principal site within the cell for the assembly and processing of macromolecules. The stacked membrane structure of the Golgi apparatus along with its interactions with the cytoskeleton and endoplasmic reticulum has...... historically made the isolation and purification of this organelle difficult. Density centrifugation has typically been used to enrich Golgi membranes from plant microsomal preparations, and aside from minor adaptations, the approach is still widely employed. Here we outline the enrichment of Golgi membranes...... from an Arabidopsis cell suspension culture that can be used to investigate the proteome of this organelle. We also provide a useful workflow for the examination of proteomic data as the result of multiple analyses. Finally, we highlight a simple technique to validate the subcellular localization...

Mass Spectrometry for Translational Proteomics: Progress and Clinical Implications

Energy Technology Data Exchange (ETDEWEB)

Baker, Erin Shammel; Liu, Tao; Petyuk, Vladislav A.; Burnum-Johnson, Kristin E.; Ibrahim, Yehia M.; Anderson, Gordon A.; Smith, Richard D.

2012-08-31

Mass spectrometry (MS)-based proteomics measurements have become increasingly utilized in a wide range of biological and biomedical applications, and have significantly enhanced the understanding of the complex and dynamic nature of the proteome and its connections to biology and diseases. While some MS techniques such as those for targeted analysis are increasingly applied with great success, others such as global quantitative analysis (for e.g. biomarker discovery) are more challenging and continue to be developed and refined to provide the desired throughput, sensitivity and/ or specificity. New MS capabilities and proteomics-based pipelines/strategies also keep enhancing for the advancement of clinical proteomics applications such as protein biomarker discovery and validation. Herein, we provide a brief review to summarize the current state of MS-based proteomics with respect to its advantages and present limitations, while highlighting its potential in future clinical applications.

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

Science.gov (United States)

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.

Scottish Women's Hospitals--the 90th anniversary of their work in Serbia.

Science.gov (United States)

Mikić, Zelimir

2005-01-01

The Scottish Women's Hospitals (SWH), a unique health institution in the history of medicine, staffed entirely by women, was founded soon after the outbreak of the First World War, August 12, 1914 in Edinburgh, by the National Union of Women's Suffrage Societies. The founder and the main driving force behind this organisation was Dr. Elsie Inglis (1864-1917). Although her proposition to the British War Office had been rejected, she offered her services to the Allies (France, Belgium, Russia and Serbia). The first 200 bed SWH unit was sent to France in November 1914, and soon after followed other units, so at the end there were 13 very well equipped SWH units working in the various theatres of war in Belgium, Serbia, Russia, Rumania and Greece. The first unit of SWH came to Serbia in early January 1915, and was located at Kragujevac. Soon after, three other SWH units arrived to Serbia and were stationed at Mladenovac, Valjevo and Lazarevac. It was an enormous help to Serbia, full of wounded and sick people, due to the dreadful typhus epidemic which was devastating the country. A large SWH unit, attached to the Southern Slav Volunteer Division, had worked on the Dobrudja front, and there were three hospitals and a special transport unit on the Salonika Front, which were all engaged in the treatment of Serbian wounded soldiers until the end of the First World War. Two other SWH units, located in France, were treating the Serbian refugees. Serving bravely and honorably on the various theatres of war, the legendary Scottish Women's Hospitals made enormous contributions to the allied war efforts, and helped Serbian people a great deal.

On the sources of uranium in some Scottish Caledonian granites

International Nuclear Information System (INIS)

Halliday, A.N.

1982-01-01

The lead isotope systematics, zircon uranium concentrations and whole-rock rubidium concentrations of 11 Scottish Caledonian granites are examined for clues to the origin of their uranium. A positive correlation between U in zircon and initial lead isotope ratios suggests that U and Pb were derived from the same source which, as some of these granites contain their U in inherited zircons, is likely to have been within the crust. It is argued, therefore, that most of the uranium in these granites had a crustal derivation but lead isotope ratios indicate that any Lewisian contribution was minor in comparison with those from postulated Grenville, Morarian or Caledonian metamorphic reservoirs. However, additional data are required before this conclusion can be extended to include uraniferous Caledonian granites such as Cairngorm. (author)

Tissue-based map of the human proteome

DEFF Research Database (Denmark)

Uhlén, Mathias; Fagerberg, Linn; Hallström, Björn M.

2015-01-01

Resolving the molecular details of proteome variation in the different tissues and organs of the human body will greatly increase our knowledge of human biology and disease. Here, we present a map of the human tissue proteome based on an integrated omics approach that involves quantitative transc...

Reforming Scottish Criminal Procedure: In Search of Process Values

Directory of Open Access Journals (Sweden)

Pamela R. Ferguson

2017-01-01

Full Text Available Recent proposals to reform Scottish criminal procedure are motivated by considerations of efficiency and accurate fact-finding, and there is little attempt to offer a normative account. This paper describes these proposals and contends that their emphasis on finding ‘the truth’ is misplaced on two distinct bases: (1 it equates erroneous acquittals to wrongful convictions, thus fails to uphold a fundamental tenet of criminal procedure, namely the particular importance of protecting the innocent against wrongful conviction; and (2 it fails to recognise the importance of non-instrumental process values which are at the heart of the adversarial criminal trial.  The paper suggests that it is only by adhering to these process values that the state maintains – and demonstrates that it maintains – its moral authority to condemn and punish offenders. Key notes: Return Directive, entry ban, illegal migrant, criminal law sanctions, crimmigration, expulsion.

Proteomic tools for environmental microbiology--a roadmap from sample preparation to protein identification and quantification.

Science.gov (United States)

Wöhlbrand, Lars; Trautwein, Kathleen; Rabus, Ralf

2013-10-01

The steadily increasing amount of (meta-)genomic sequence information of diverse organisms and habitats has a strong impact on research in microbial physiology and ecology. In-depth functional understanding of metabolic processes and overall physiological adaptation to environmental changes, however, requires application of proteomics, as the context specific proteome constitutes the true functional output of a cell. Considering the enormous structural and functional diversity of proteins, only rational combinations of various analytical approaches allow a holistic view on the overall state of the cell. Within the past decade, proteomic methods became increasingly accessible to microbiologists mainly due to the robustness of analytical methods (e.g. 2DE), and affordability of mass spectrometers and their relative ease of use. This review provides an overview on the complex portfolio of state-of-the-art proteomics and highlights the basic principles of key methods, ranging from sample preparation of laboratory or environmental samples, via protein/peptide separation (gel-based or gel-free) and different types of mass spectrometric protein/peptide analyses, to protein identification and abundance determination. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Plant redox proteomics

DEFF Research Database (Denmark)

Navrot, Nicolas; Finnie, Christine; Svensson, Birte

2011-01-01

PTMs in regulating enzymatic activities and controlling biological processes in plants. Notably, proteins controlling the cellular redox state, e.g. thioredoxin and glutaredoxin, appear to play dual roles to maintain oxidative stress resistance and regulate signal transduction pathways via redox PTMs......In common with other aerobic organisms, plants are exposed to reactive oxygen species resulting in formation of post-translational modifications related to protein oxidoreduction (redox PTMs) that may inflict oxidative protein damage. Accumulating evidence also underscores the importance of redox....... To get a comprehensive overview of these types of redox-regulated pathways there is therefore an emerging interest to monitor changes in redox PTMs on a proteome scale. Compared to some other PTMs, e.g. protein phosphorylation, redox PTMs have received less attention in plant proteome analysis, possibly...

The use of combined techniques: Scottish showers, hot bath and manual techniques in the treatment of migraine headache

Directory of Open Access Journals (Sweden)

Andrei-Cătălin Ionițe

2017-12-01

Full Text Available Migraines are caused by internal factors (out of which the most important are genetically and physiologically determined and the external ones, namely, the environment. The most common factor which triggers the migraines is the physiological one. According to some specialized studies, in most cases, it is assumed that migraines are caused by a neuro-vascular disorder. This statement works as a compromise solution for the two theories supported by specialists, which explain the occurrence of migraines: neural mechanisms theory and the theory of vascular origin. Starting from these two theories, we’ve used Scottish showers, hot baths (37oC followed by manual drainage of the venous sinuses. The Scottish showers determine the toning of the muscle capillaries. Immersion in warm water for 15 minutes determines vasodilation, along with muscle and mental relaxation. Drainage techniques of venous sinuses operate on the reciprocal tension membranes (RTM, restoring their mobility and improving neuro-vascular disorders. In this research, there were involved 3 subjects, who have taken part in the treatment sessions; they have been monitored and the resulting data has been recorded.

129I/127I ratios in Scottish coastal surface sea water: Geographical and temporal responses to changing emissions

International Nuclear Information System (INIS)

Schnabel, Christoph; Olive, Valerie; Atarashi-Andoh, Mariko; Dougans, Andrew; Ellam, Robert M.; Freeman, Stewart; Maden, Colin; Stocker, Martin; Synal, Hans-Arno; Wacker, Lukas; Xu Sheng

2007-01-01

This work constitutes the first survey of I isotope ratios for Scottish sea water including the first data for the west of Scotland. These data are of importance because of the proximity to the world's second largest emission source of 129 I to the sea, the Sellafield nuclear reprocessing plant, because of the increasing importance of the sea to land transfer of 129 I and also as input data for dose estimates based on this pathway of 129 I. 129 I/ 127 I ratios in SW Scotland reached 3 x 10 -6 in 2004. No strong variation of I isotope ratios was found from 2003 to 2005 in Scottish sea waters. Iodine isotope ratios increased by about a factor of 6 from 1992 to 2003 in NE Scotland, in agreement with the increase of liquid 129 I emissions from Sellafield over that time period. It is demonstrated that 129 I/ 127 I ratios agree better than 129 I concentrations for samples from similar locations taken in very close temporal proximity, indicating that this ratio is more appropriate to interpret than the radionuclide concentration

Agri-food supply chains and sustainability-related issues: evidence from across the Scottish agri-food economy

OpenAIRE

Leat, Philip M.K.; Lamprinopoulou-Kranis, Chrysa; Revoredo-Giha, Cesar; Kupiec-Teahan, Beata

2011-01-01

This paper examines the influence of agri-food supply chains on the sustainability-related activities and decisions of Scottish farmers, as well as the treatment of sustainability issues by food processors and retailers themselves. It is based on 8 whole chain case studies covering some of Scotland’s major agricultural products. The cases identify differing levels of understanding and activities related to sustainability, but widespread acknowledgement that sustainability involves the develop...

Golgi enrichment and proteomic analysis of developing Pinus radiata xylem by free-flow electrophoresis.

Directory of Open Access Journals (Sweden)

Harriet T Parsons

Full Text Available 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.

Comprehensive Proteomic Analysis of Human Milk-derived Extracellular Vesicles Unveils a Novel Functional Proteome Distinct from Other Milk Components*

Science.gov (United States)

van Herwijnen, Martijn J.C.; Zonneveld, Marijke I.; Goerdayal, Soenita; Nolte – 't Hoen, Esther N.M.; Garssen, Johan; Stahl, Bernd; Maarten Altelaar, A.F.; Redegeld, Frank A.; Wauben, Marca H.M.

2016-01-01

Breast milk contains several macromolecular components with distinctive functions, whereby milk fat globules and casein micelles mainly provide nutrition to the newborn, and whey contains molecules that can stimulate the newborn's developing immune system and gastrointestinal tract. Although extracellular vesicles (EV) have been identified in breast milk, their physiological function and composition has not been addressed in detail. EV are submicron sized vehicles released by cells for intercellular communication via selectively incorporated lipids, nucleic acids, and proteins. Because of the difficulty in separating EV from other milk components, an in-depth analysis of the proteome of human milk-derived EV is lacking. In this study, an extensive LC-MS/MS proteomic analysis was performed of EV that had been purified from breast milk of seven individual donors using a recently established, optimized density-gradient-based EV isolation protocol. A total of 1963 proteins were identified in milk-derived EV, including EV-associated proteins like CD9, Annexin A5, and Flotillin-1, with a remarkable overlap between the different donors. Interestingly, 198 of the identified proteins are not present in the human EV database Vesiclepedia, indicating that milk-derived EV harbor proteins not yet identified in EV of different origin. Similarly, the proteome of milk-derived EV was compared with that of other milk components. For this, data from 38 published milk proteomic studies were combined in order to construct the total milk proteome, which consists of 2698 unique proteins. Remarkably, 633 proteins identified in milk-derived EV have not yet been identified in human milk to date. Interestingly, these novel proteins include proteins involved in regulation of cell growth and controlling inflammatory signaling pathways, suggesting that milk-derived EVs could support the newborn's developing gastrointestinal tract and immune system. Overall, this study provides an expansion of

Comprehensive Proteomic Analysis of Human Milk-derived Extracellular Vesicles Unveils a Novel Functional Proteome Distinct from Other Milk Components.

Science.gov (United States)

van Herwijnen, Martijn J C; Zonneveld, Marijke I; Goerdayal, Soenita; Nolte-'t Hoen, Esther N M; Garssen, Johan; Stahl, Bernd; Maarten Altelaar, A F; Redegeld, Frank A; Wauben, Marca H M

2016-11-01

Breast milk contains several macromolecular components with distinctive functions, whereby milk fat globules and casein micelles mainly provide nutrition to the newborn, and whey contains molecules that can stimulate the newborn's developing immune system and gastrointestinal tract. Although extracellular vesicles (EV) have been identified in breast milk, their physiological function and composition has not been addressed in detail. EV are submicron sized vehicles released by cells for intercellular communication via selectively incorporated lipids, nucleic acids, and proteins. Because of the difficulty in separating EV from other milk components, an in-depth analysis of the proteome of human milk-derived EV is lacking. In this study, an extensive LC-MS/MS proteomic analysis was performed of EV that had been purified from breast milk of seven individual donors using a recently established, optimized density-gradient-based EV isolation protocol. A total of 1963 proteins were identified in milk-derived EV, including EV-associated proteins like CD9, Annexin A5, and Flotillin-1, with a remarkable overlap between the different donors. Interestingly, 198 of the identified proteins are not present in the human EV database Vesiclepedia, indicating that milk-derived EV harbor proteins not yet identified in EV of different origin. Similarly, the proteome of milk-derived EV was compared with that of other milk components. For this, data from 38 published milk proteomic studies were combined in order to construct the total milk proteome, which consists of 2698 unique proteins. Remarkably, 633 proteins identified in milk-derived EV have not yet been identified in human milk to date. Interestingly, these novel proteins include proteins involved in regulation of cell growth and controlling inflammatory signaling pathways, suggesting that milk-derived EVs could support the newborn's developing gastrointestinal tract and immune system. Overall, this study provides an expansion of

Hydrops associated with chondrodysplasia of the fetus in a miniature Scottish Highland cow.

Science.gov (United States)

Catalina Cabrera, L; McNabb, Bret R; Woods, Sarah E; Cartoceti, Andrew N; Busch, Rosie C

2016-03-01

CASE DESCRIPTION A 2-year-old primiparous miniature Scottish Highland cow with an unknown breeding date was evaluated for suspected hydrops. CLINICAL FINDINGS Transabdominal and transrectal ultrasonographic examination identified a large amount of hypoechoic fluid within an enlarged uterus; the fetus could not be identified. Presence of a severely distended uterus and concerns regarding associated health risks to the cow led to the decision to induce labor. Although fluids were expelled, parturition did not progress further over the following 48 hours. Vaginal examination revealed a partially dilated cervix and an abnormally shaped fetus that was too large to pass vaginally. TREATMENT AND OUTCOME Supportive care was provided to the cow, and a stillborn bull calf was delivered by cesarean section. Grossly evident chondrodystrophic dwarfism with hydrocephalus, compatible with so-called bulldog calf malformations, was confirmed by diagnostic imaging and histopathologic evaluation. The cow recovered from surgery uneventfully and was discharged from the hospital the following day. Genetic analysis of DNA from hair roots collected from the sire and dam confirmed both were carriers of an aggrecan-1 gene mutation (bulldog dwarfism1) previously associated with dwarfism and bulldog calf malformations in Dexter cattle. CLINICAL RELEVANCE To our knowledge, this is the first reported case of bulldog calf malformations associated with an aggrecan-1 gene mutation in miniature Scottish Highland cattle, confirming that at least 1 genetic mutation associated with this condition is found in cattle breeds other than Dexter. The findings highlighted the clinical importance of testing for known genetic diseases in breeding cattle, particularly among miniature breeds.

Comparative proteomics analysis of oral cancer cell lines: identification of cancer associated proteins

Science.gov (United States)

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

PatternLab for proteomics: a tool for differential shotgun proteomics

Directory of Open Access Journals (Sweden)

Yates John R

2008-07-01

Full Text Available Abstract Background A goal of proteomics is to distinguish between states of a biological system by identifying protein expression differences. Liu et al. demonstrated a method to perform semi-relative protein quantitation in shotgun proteomics data by correlating the number of tandem mass spectra obtained for each protein, or "spectral count", with its abundance in a mixture; however, two issues have remained open: how to normalize spectral counting data and how to efficiently pinpoint differences between profiles. Moreover, Chen et al. recently showed how to increase the number of identified proteins in shotgun proteomics by analyzing samples with different MS-compatible detergents while performing proteolytic digestion. The latter introduced new challenges as seen from the data analysis perspective, since replicate readings are not acquired. Results To address the open issues above, we present a program termed PatternLab for proteomics. This program implements existing strategies and adds two new methods to pinpoint differences in protein profiles. The first method, ACFold, addresses experiments with less than three replicates from each state or having assays acquired by different protocols as described by Chen et al. ACFold uses a combined criterion based on expression fold changes, the AC test, and the false-discovery rate, and can supply a "bird's-eye view" of differentially expressed proteins. The other method addresses experimental designs having multiple readings from each state and is referred to as nSVM (natural support vector machine because of its roots in evolutionary computing and in statistical learning theory. Our observations suggest that nSVM's niche comprises projects that select a minimum set of proteins for classification purposes; for example, the development of an early detection kit for a given pathology. We demonstrate the effectiveness of each method on experimental data and confront them with existing strategies

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

Science.gov (United States)

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…

Clinical proteomic analysis of scrub typhus infection.

Science.gov (United States)

Park, Edmond Changkyun; Lee, Sang-Yeop; Yun, Sung Ho; Choi, Chi-Won; Lee, Hayoung; Song, Hyun Seok; Jun, Sangmi; Kim, Gun-Hwa; Lee, Chang-Seop; Kim, Seung Il

2018-01-01

Scrub typhus is an acute and febrile infectious disease caused by the Gram-negative α-proteobacterium Orientia tsutsugamushi from the family Rickettsiaceae that is widely distributed in Northern, Southern and Eastern Asia. In the present study, we analysed the serum proteome of scrub typhus patients to investigate specific clinical protein patterns in an attempt to explain pathophysiology and discover potential biomarkers of infection. Serum samples were collected from three patients (before and after treatment with antibiotics) and three healthy subjects. One-dimensional sodium dodecyl sulphate-polyacrylamide gel electrophoresis followed by liquid chromatography-tandem mass spectrometry was performed to identify differentially abundant proteins using quantitative proteomic approaches. Bioinformatic analysis was then performed using Ingenuity Pathway Analysis. Proteomic analysis identified 236 serum proteins, of which 32 were differentially expressed in normal subjects, naive scrub typhus patients and patients treated with antibiotics. Comparative bioinformatic analysis of the identified proteins revealed up-regulation of proteins involved in immune responses, especially complement system, following infection with O. tsutsugamushi , and normal expression was largely rescued by antibiotic treatment. This is the first proteomic study of clinical serum samples from scrub typhus patients. Proteomic analysis identified changes in protein expression upon infection with O. tsutsugamushi and following antibiotic treatment. Our results provide valuable information for further investigation of scrub typhus therapy and diagnosis.

Proteomic interrogation of human chromatin.

Directory of Open Access Journals (Sweden)

Mariana P Torrente

Full Text Available Chromatin proteins provide a scaffold for DNA packaging and a basis for epigenetic regulation and genomic maintenance. Despite understanding its functional roles, mapping the chromatin proteome (i.e. the "Chromatome" is still a continuing process. Here, we assess the biological specificity and proteomic extent of three distinct chromatin preparations by identifying proteins in selected chromatin-enriched fractions using mass spectrometry-based proteomics. These experiments allowed us to produce a chromatin catalog, including several proteins ranging from highly abundant histone proteins to less abundant members of different chromatin machinery complexes. Using a Normalized Spectral Abundance Factor approach, we quantified relative abundances of the proteins across the chromatin enriched fractions giving a glimpse into their chromosomal abundance. The large-scale data sets also allowed for the discovery of a variety of novel post-translational modifications on the identified chromatin proteins. With these comparisons, we find one of the probed methods to be qualitatively superior in specificity for chromatin proteins, but inferior in proteomic extent, evidencing a compromise that must be made between biological specificity and broadness of characterization. Additionally, we attempt to identify proteins in eu- and heterochromatin, verifying the enrichments by characterizing the post-translational modifications detected on histone proteins from these chromatin regions. In summary, our results provide insights into the value of different methods to extract chromatin-associated proteins and provide starting points to study the factors that may be involved in directing gene expression and other chromatin-related processes.

Schistosomiasis in Scottish travellers: public health importance of laboratory testing and the need for enhanced surveillance.

Science.gov (United States)

Alexander, Claire L; Cottom, Laura; Smith, Kitty; Perrow, Kali; Coyne, Michael; Jones, Brian L

2018-03-01

Imported schistosomiasis is of significant public health importance and is likely to be underestimated since infection is often asymptomatic. We describe data from travellers residing in Scotland which includes a subset of group travellers from one of the largest Health Boards in Scotland. Clotted bloods were obtained during the period 2001-15 from a total of 8163 Scottish travellers. This included seven groups comprising of 182 travellers. Sera were examined for the presence of Schistosome species antibody at the Scottish Parasite Diagnostic and Reference Laboratory (SPDRL). Of all, 25% (n = 1623) tested positive with 40% (n = 651) of those patients aged between 20 and 24 years. Although 62% (n = 1006) of those who tested positive reported travel to Africa, important information on the specific region visited was lacking in almost one-third of samples received. Overall, 62 (34%) of group travellers tested positive and 95% (n = 59) reporting travel to Africa. Globalization, affordable air travel and improved awareness, are likely to contribute towards the increasing number of imported schistosomiasis cases. Therefore, enhanced surveillance capturing detailed travel history and fresh water exposures will improve risk stratification, pre-travel advice and optimize testing and treatment regimes for this increasingly important parasitic disease.

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

Science.gov (United States)

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.

Is there a relationship between the food intakes of Scottish 5(1/2)-8(1/2)-year-olds and those of their mothers?

Science.gov (United States)

Longbottom, P J; Wrieden, W L; Pine, C M

2002-08-01

Recent reports have highlighted certain aspects of the diets of children and adults in Scotland today that are a cause for concern. If there are significant associations between family members in food choice and thus in nutrient intakes, this may be important in the aetiology and prevention of diseases relating to dietary risk factors. To compare the food intake of Scottish children aged 5(1/2)-8(1/2) years with that of their mothers. As part of a larger study, data on food intakes were obtained from 4-day weighed food records for 36 Scottish children (12 boys and 24 girls), aged 5(1/2)-8(1/2) years, who had participated in the 1992/1993 National Diet and Nutrition Survey (NDNS), and their mothers. Compared with their mothers, children had higher median densities [weight (g) of foods per 4.2 MJ (1000 kcal)] of snack foods including fruit, bread and confectionery and lower median densities of meat and meat products, fish, potatoes and vegetables. Positive, significant correlations between children and mothers were found for median densities of bread (r = 0.360, P foods that should be reduced in the average Scottish diet. Children's intakes of snack foods were correlated with that of their mothers emphasizing the need for change at a family level if current guidelines on diet are to be implemented.

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

Science.gov (United States)

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.

Prevalence of overweight and obesity among nurses in Scotland: A cross-sectional study using the Scottish Health Survey.

Science.gov (United States)

Kyle, Richard G; Neall, Rosie A; Atherton, Iain M

2016-01-01

Increasing prevalence of overweight and obesity represents a global pandemic. As the largest occupational group in international healthcare systems nurses are at the forefront of health promotion to address this pandemic. However, nurses own health behaviours are known to influence the extent to which they engage in health promotion and the public's confidence in advice offered. Estimating the prevalence of overweight and obesity among nurses is therefore important. However, to date, prevalence estimates have been based on non-representative samples and internationally no studies have compared prevalence of overweight and obesity among nurses to other healthcare professionals using representative data. To estimate overweight and obesity prevalence among nurses in Scotland, and compare to other healthcare professionals and those working in non-heath related occupations. Cross-sectional study using a nationally representative sample of five aggregated annual rounds (2008-2012) of the Scottish Health Survey. Scotland. 13,483 adults aged 17-65 indicating they had worked in the past 4 weeks, classified in four occupational groups: nurses (n=411), other healthcare professionals (n=320), unqualified care staff (n=685), and individuals employed in non-health related occupations (n=12,067). Prevalence of overweight and obesity defined as Body Mass Index≥25.0. Estimates of overweight and obesity prevalence in each occupational group were calculated with 95% confidence intervals (CI). A logistic regression model was then built to compare the odds of being overweight or obese with not being overweight or obese for nurses in comparison to the other occupational categories. Data were analysed using SAS 9.1.3. 69.1% (95% CI 64.6, 73.6) of Scottish nurses were overweight or obese. Prevalence of overweight and obesity was higher in nurses than other healthcare professionals (51.3%, CI 45.8, 56.7), unqualified care staff (68.5%, CI 65.0, 72.0) and those in non-health related

The state of proteome profiling in the fungal genus Aspergillus.

Science.gov (United States)

Kim, Yonghyun; Nandakumar, M P; Marten, Mark R

2008-03-01

Aspergilli are an important genus of filamentous fungi that contribute to a multibillion dollar industry. Since many fungal genome sequencing were recently completed, it would be advantageous to profile their proteome to better understand the fungal cell factory. Here, we review proteomic data generated for the Aspergilli in recent years. Thus far, a combined total of 28 cell surface, 102 secreted and 139 intracellular proteins have been identified based on 10 different studies on Aspergillus proteomics. A summary proteome map highlighting identified proteins in major metabolic pathway is presented.

Share and share alike: encouraging the reuse of academic resources through the Scottish electronic Staff Development Library

Directory of Open Access Journals (Sweden)

Lorna M. Campbell

2001-12-01

Full Text Available The Scottish electronic Staff Development Library (http://www.sesdl.scotcit.acuk is an ongoing collaborative project involving the Universities of Edinburgh, Paisley and Strathclyde which has been funded by SHEFC as part of their current ScotCIT Programme (http:llwww.scotcit.ac.uk. This project is being developed in response to the increasing demand for flexible, high-quality staff development materials.

Scientific Workflow Management in Proteomics

Science.gov (United States)

de Bruin, Jeroen S.; Deelder, André M.; Palmblad, Magnus

2012-01-01

Data processing in proteomics can be a challenging endeavor, requiring extensive knowledge of many different software packages, all with different algorithms, data format requirements, and user interfaces. In this article we describe the integration of a number of existing programs and tools in Taverna Workbench, a scientific workflow manager currently being developed in the bioinformatics community. We demonstrate how a workflow manager provides a single, visually clear and intuitive interface to complex data analysis tasks in proteomics, from raw mass spectrometry data to protein identifications and beyond. PMID:22411703

PROTEOMICS in aquaculture

DEFF Research Database (Denmark)

Rodrigues, Pedro M.; Silva, Tomé S.; Dias, Jorge

2012-01-01

Over the last forty years global aquaculture presented a growth rate of 6.9% per annum with an amazing production of 52.5million tonnes in 2008, and a contribution of 43% of aquatic animal food for human consumption. In order to meet the world's health requirements of fish protein, a continuous...... growth in production is still expected for decades to come. Aquaculture is, though, a very competitive market, and a global awareness regarding the use of scientific knowledge and emerging technologies to obtain a better farmed organism through a sustainable production has enhanced the importance...... questions and the role of proteomics in their investigation, outlining the advantages, disadvantages and future challenges. A brief description of the proteomics technical approaches will be presented. Special focus will be on the latest trends related to the aquaculture production of fish with defined...

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

Science.gov (United States)

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…

Implementation of proteomics for cancer research: past, present, and future.

Science.gov (United States)

Karimi, Parisa; Shahrokni, Armin; Ranjbar, Mohammad R Nezami

2014-01-01

Cancer is the leading cause of the death, accounts for about 13% of all annual deaths worldwide. Many different fields of science are collaborating together studying cancer to improve our knowledge of this lethal disease, and find better solutions for diagnosis and treatment. Proteomics is one of the most recent and rapidly growing areas in molecular biology that helps understanding cancer from an omics data analysis point of view. The human proteome project was officially initiated in 2008. Proteomics enables the scientists to interrogate a variety of biospecimens for their protein contents and measure the concentrations of these proteins. Current necessary equipment and technologies for cancer proteomics are mass spectrometry, protein microarrays, nanotechnology and bioinformatics. In this paper, we provide a brief review on proteomics and its application in cancer research. After a brief introduction including its definition, we summarize the history of major previous work conducted by researchers, followed by an overview on the role of proteomics in cancer studies. We also provide a list of different utilities in cancer proteomics and investigate their advantages and shortcomings from theoretical and practical angles. Finally, we explore some of the main challenges and conclude the paper with future directions in this field.

Positional proteomics in the era of the human proteome project on the doorstep of precision medicine.

Science.gov (United States)

Eckhard, Ulrich; Marino, Giada; Butler, Georgina S; Overall, Christopher M

2016-03-01

Proteolytic processing is a pervasive and irreversible post-translational modification that expands the protein universe by generating new proteoforms (protein isoforms). Unlike signal peptide or prodomain removal, protease-generated proteoforms can rarely be predicted from gene sequences. Positional proteomic techniques that enrich for N- or C-terminal peptides from proteomes are indispensable for a comprehensive understanding of a protein's function in biological environments since protease cleavage frequently results in altered protein activity and localization. Proteases often process other proteases and protease inhibitors which perturbs proteolytic networks and potentiates the initial cleavage event to affect other molecular networks and cellular processes in physiological and pathological conditions. This review is aimed at researchers with a keen interest in state of the art systems level positional proteomic approaches that: (i) enable the study of complex protease-protease, protease-inhibitor and protease-substrate crosstalk and networks; (ii) allow the identification of proteolytic signatures as candidate disease biomarkers; and (iii) are expected to fill the Human Proteome Project missing proteins gap. We predict that these methodologies will be an integral part of emerging precision medicine initiatives that aim to customize healthcare, converting reactive medicine into a personalized and proactive approach, improving clinical care and maximizing patient health and wellbeing, while decreasing health costs by eliminating ineffective therapies, trial-and-error prescribing, and adverse drug effects. Such initiatives require quantitative and functional proteome profiling and dynamic disease biomarkers in addition to current pharmacogenomics approaches. With proteases at the pathogenic center of many diseases, high-throughput protein termini identification techniques such as TAILS (Terminal Amine Isotopic Labeling of Substrates) and COFRADIC (COmbined

Comparative proteomic analysis in Miscanthus sinensis exposed to antimony stress

International Nuclear Information System (INIS)

Xue, Liang; Ren, Huadong; Li, Sheng; Gao, Ming; Shi, Shengqing; Chang, Ermei; Wei, Yuan; Yao, Xiaohua; Jiang, Zeping; Liu, Jianfeng

2015-01-01

To explore the molecular basis of Sb tolerance mechanism in plant, a comparative proteomic analysis of both roots and leaves in Miscanthus sinensis has been conducted in combination with physiological and biochemical analyses. M. sinensis seedlings were exposed to different doses of Sb, and both roots and leaves were collected after 3 days of treatment. Two-dimensional gel electrophoresis (2-DE) and image analyses found that 29 protein spots showed 1.5-fold change in abundance in leaves and 19 spots in roots, of which 31 were identified by MALDI-TOF-MS and MALDI-TOF-TOF-MS. Proteins involved in antioxidant defense and stress response generally increased their expression all over the Sb treatments. In addition, proteins relative to transcription, signal transduction, energy metabolism and cell division and cell structure showed a variable expression pattern over Sb concentrations. Overall these findings provide new insights into the probable survival mechanisms by which M. sinensis could be adapting to Sb phytotoxicity. - Highlights: • Proteomics in Miscanthus sinensis leaves and roots exposed to Sb stress were studied. • There were 31 spots that were identified by mass spectrometry. • Most of these proteins were involved in antioxidant defense and stress response. • Our findings provide new insights into the tolerant mechanisms to Sb stress. - Miscanthus sinensis proteomic analysis under Sb stress reveals probable molecular mechanisms on Sb detoxification

The Proteomics Big Challenge for Biomarkers and New Drug-Targets Discovery

Science.gov (United States)

Savino, Rocco; Paduano, Sergio; Preianò, Mariaimmacolata; Terracciano, Rosa

2012-01-01

In the modern process of drug discovery, clinical, functional and chemical proteomics can converge and integrate synergies. Functional proteomics explores and elucidates the components of pathways and their interactions which, when deregulated, lead to a disease condition. This knowledge allows the design of strategies to target multiple pathways with combinations of pathway-specific drugs, which might increase chances of success and reduce the occurrence of drug resistance. Chemical proteomics, by analyzing the drug interactome, strongly contributes to accelerate the process of new druggable targets discovery. In the research area of clinical proteomics, proteome and peptidome mass spectrometry-profiling of human bodily fluid (plasma, serum, urine and so on), as well as of tissue and of cells, represents a promising tool for novel biomarker and eventually new druggable targets discovery. In the present review we provide a survey of current strategies of functional, chemical and clinical proteomics. Major issues will be presented for proteomic technologies used for the discovery of biomarkers for early disease diagnosis and identification of new drug targets. PMID:23203042

Single muscle fiber proteomics reveals unexpected mitochondrial specialization

DEFF Research Database (Denmark)

Murgia, Marta; Nagaraj, Nagarjuna; Deshmukh, Atul S

2015-01-01

and unbiased proteomics methods yielded the same subtype assignment. We discovered novel subtype-specific features, most prominently mitochondrial specialization of fiber types in substrate utilization. The fiber type-resolved proteomes can be applied to a variety of physiological and pathological conditions...

Shaping Biological Knowledge: Applications in Proteomics

Directory of Open Access Journals (Sweden)

R. Appel

2006-04-01

Full Text Available The central dogma of molecular biology has provided a meaningful principle for data integration in the field of genomics. In this context, integration reflects the known transitions from a chromosome to a protein sequence: transcription, intron splicing, exon assembly and translation. There is no such clear principle for integrating proteomics data, since the laws governing protein folding and interactivity are not quite understood. In our effort to bring together independent pieces of information relative to proteins in a biologically meaningful way, we assess the bias of bioinformatics resources and consequent approximations in the framework of small-scale studies. We analyse proteomics data while following both a data-driven (focus on proteins smaller than 10 kDa and a hypothesis-driven (focus on whole bacterial proteomes approach. These applications are potentially the source of specialized complements to classical biological ontologies.

Shaping biological knowledge: applications in proteomics.

Science.gov (United States)

Lisacek, F; Chichester, C; Gonnet, P; Jaillet, O; Kappus, S; Nikitin, F; Roland, P; Rossier, G; Truong, L; Appel, R

2004-01-01

The central dogma of molecular biology has provided a meaningful principle for data integration in the field of genomics. In this context, integration reflects the known transitions from a chromosome to a protein sequence: transcription, intron splicing, exon assembly and translation. There is no such clear principle for integrating proteomics data, since the laws governing protein folding and interactivity are not quite understood. In our effort to bring together independent pieces of information relative to proteins in a biologically meaningful way, we assess the bias of bioinformatics resources and consequent approximations in the framework of small-scale studies. We analyse proteomics data while following both a data-driven (focus on proteins smaller than 10 kDa) and a hypothesis-driven (focus on whole bacterial proteomes) approach. These applications are potentially the source of specialized complements to classical biological ontologies.

Proteomics of apheresis platelet supernatants during routine storage: Gender-related differences.

Science.gov (United States)

Dzieciatkowska, Monika; D'Alessandro, Angelo; Burke, Timothy A; Kelher, Marguerite R; Moore, Ernest E; Banerjee, Anirban; Silliman, Christopher C; West, Bernadette F; Hansen, Kirk C

2015-01-01

Proteomics has identified potential pathways involved in platelet storage lesions, which correlate with untoward effects in the recipient, including febrile non-haemolytic reactions. We hypothesize that an additional pathway involves protein mediators that accumulate in the platelet supernatants during routine storage in a donor gender-specific fashion. Apheresis platelet concentrates were collected from 5 healthy males and 5 females and routinely stored. The 14 most abundant plasma proteins were removed and the supernatant proteins from days 1 and 5 were analyzed via 1D-SDS-PAGE/nanoLC-MS/MS, before label-free quantitative proteomics analyses. Findings from a subset of 18 proteins were validated via LC-SRM analyses against stable isotope labeled standards. A total of 503 distinct proteins were detected in the platelet supernatants from the 4 sample groups: female or male donor platelets, either at storage day 1 or 5. Proteomics suggested a storage and gender-dependent impairment of blood coagulation mediators, pro-inflammatory complement components and cytokines, energy and redox metabolic enzymes. The supernatants from female donors demonstrated increased deregulation of structural proteins, extracellular matrix proteins and focal adhesion proteins, possibly indicating storage-dependent platelet activation. Routine storage of platelet concentrates induces changes in the supernatant proteome, which may have effects on the transfused patient, some of which are related to donor gender. The rationale behind this study is that protein components in platelet releasates have been increasingly observed to play a key role in adverse events and impaired homeostasis in transfused recipients. In this view, proteomics has recently emerged as a functional tool to address the issue of protein composition of platelet releasates from buffy coat-derived platelet concentrates in the blood bank. Despite early encouraging studies on buffy coat-derived platelet concentrates, platelet

Identification and characterization of N-glycosylated proteins using proteomics

DEFF Research Database (Denmark)

Selby, David S; Larsen, Martin R; Calvano, Cosima Damiana

2008-01-01

and analysis of glycoproteins and glycopeptides. Combinations of affinity-enrichment techniques, chemical and biochemical protocols, and advanced mass spectrometry facilitate detailed glycoprotein analysis in proteomics, from fundamental biological studies to biomarker discovery in biomedicine....... is a complex task and is currently achieved by mass spectrometry-based methods that enable identification of glycoproteins and localization, classification, and analysis of individual glycan structures on proteins. In this chapter we briefly introduce a range of analytical technologies for recovery...

Bayesian methods for proteomic biomarker development

Directory of Open Access Journals (Sweden)

Belinda Hernández

2015-12-01

In this review we provide an introduction to Bayesian inference and demonstrate some of the advantages of using a Bayesian framework. We summarize how Bayesian methods have been used previously in proteomics and other areas of bioinformatics. Finally, we describe some popular and emerging Bayesian models from the statistical literature and provide a worked tutorial including code snippets to show how these methods may be applied for the evaluation of proteomic biomarkers.

Towards high throughput and spatiotemporal proteomics : analytical workflows and quantitative label-free mass spectrometry

NARCIS (Netherlands)

Mostovenko, Ekaterina

2013-01-01

A large part of modern biology is dedicated to the functional annotation and interpretation of genetic information and its influence on the subject’s phenotype. Proteomics describes the state of the system from the perspective of expression, structure, localization, interaction and function of the

Serious shortcomings in the management of children with anaphylaxis in Scottish schools.

Directory of Open Access Journals (Sweden)

Kirsty E Rankin

2006-08-01

Full Text Available BACKGROUND: The United Kingdom incidence of anaphylaxis has increased very sharply over the last decade, with the highest rates of hospital admissions occurring in school-aged children. This raises concerns about the extent to which schools are aware of approaches to the prevention and treatment of anaphylaxis. METHODS AND FINDINGS: We undertook a national postal survey of 250 Scottish schools enquiring about approaches to managing children considered to be at risk of anaphylaxis. We obtained responses from 148 (60% schools, 90 (61% of which reported having at least one at risk child. Most (80% schools with children considered to be at risk reported having personalised care plans and invariably reported having at least one member of staff trained in the emergency treatment of anaphylaxis. Access to adrenaline was available on-site in 97% of these schools. However, significantly fewer schools without children considered to be at risk reported having a trained member of staff (48%, p < 0.001, with access to adrenaline being very poor (12%, p < 0.001. Overall, 59% of respondents did not feel confident in their school's ability to respond in an emergency situation. CONCLUSIONS: Most schools with children considered to be at risk of anaphylaxis report using personal care plans and having a member of staff trained in the use of, and with access to, adrenaline. The picture is, however, less encouraging in schools without known at risk children, both in relation to staff training and access to adrenaline. The majority of schools with at risk children have poorly developed strategies for preventing food-triggered anaphylaxis reactions. There is a need for detailed national guidelines for all schools, which the Scottish Executive must now ensure are developed and implemented.

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

Science.gov (United States)

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…

Data set for the proteomic inventory and quantitative analysis of chicken uterine fluid during eggshell biomineralization

Directory of Open Access Journals (Sweden)

Pauline Marie

2014-12-01

Full Text Available Chicken eggshell is the protective barrier of the egg. It is a biomineral composed of 95% calcium carbonate on calcitic form and 3.5% organic matrix proteins. Mineralization process occurs in uterus into the uterine fluid. This acellular fluid contains ions and organic matrix proteins precursors which are interacting with the mineral phase and control crystal growth, eggshell structure and mechanical properties. We performed a proteomic approach and identified 308 uterine fluid proteins. Gene Ontology terms enrichments were determined to investigate their potential functions. Mass spectrometry analyses were also combined to label free quantitative analysis to determine the relative abundance of 96 proteins at initiation, rapid growth phase and termination of shell calcification. Sixty four showed differential abundance according to the mineralization stage. Their potential functions have been annotated. The complete proteomic, bioinformatic and functional analyses are reported in Marie et al., J. Proteomics (2015 [1].

Falls in Scottish homicide: lessons for homicide reduction in mental health patients

Science.gov (United States)

Crichton, John H. M.

2017-01-01

The sustained fall in Scottish homicide rates follows crime reduction measures informed by the epidemiology of suicide. The violence reduction unit targeted young men carrying knives in public. The restriction of weapons immediately to hand appears to have caused an absolute fall in homicide just as suicide reduction was observed following changes to domestic gas supply. Further homicide reduction may be accomplished in the domestic setting with targeted changes in kitchen knife design in home safety planning for high-risk households. Most commonly homicides involving those in recent contact with mental health services in the UK have domestic characteristics and similar safety planning may be targeted at those with mental disorder and a history of violence. PMID:28811910

Proteomics and circadian rhythms: It’s all about signaling!

Science.gov (United States)

Mauvoisin, Daniel; Dayon, Loïc; Gachon, Frédéric; Kussmann, Martin

2014-01-01

1. Abstract Proteomic technologies using mass spectrometry (MS) offer new perspectives in circadian biology, in particular the possibility to study posttranslational modifications (PTMs). To date, only very few studies have been carried out to decipher the rhythmicity of protein expression in mammals with large-scale proteomics. Although signaling has been shown to be of high relevance, comprehensive characterization studies of PTMs are even more rare. This review aims at describing the actual landscape of circadian proteomics and the opportunities and challenges appearing on the horizon. Emphasis was given to signaling processes for their role in metabolic heath as regulated by circadian clocks and environmental factors. Those signaling processes are expected to be better and more deeply characterized in the coming years with proteomics. PMID:25103677

Soybean Proteome Database 2012: Update on the comprehensive data repository for soybean proteomics

Directory of Open Access Journals (Sweden)

Hajime eOhyanagi

2012-05-01

Full Text Available The Soybean Proteome Database (SPD was created to provide a data repository for functional analyses of soybean responses to flooding stress, thought to be a major constraint for establishment and production of this plant. Since the last publication of the SPD, we thoroughly enhanced the contents of database, particularly protein samples and their annotations from several organelles. The current release contains 23 reference maps of soybean (Glycine max cv. Enrei proteins collected from several organs, tissues and organelles including the maps for plasma membrane, cell wall, chloroplast and mitochondrion, which were electrophoresed on two-dimensional polyacrylamide gels. Furthermore, the proteins analyzed with gel-free proteomics technique have been added and available online. In addition to protein fluctuations under flooding, those of salt and drought stress have been included in the current release. An omics table also has been provided to reveal relationships among mRNAs, proteins and metabolites with a unified temporal-profile tag in order to facilitate retrieval of the data based on the temporal profiles. An intuitive user interface based on dynamic HTML enables users to browse the network as well as the profiles of multiple omes in an integrated fashion. The SPD is available at: http://proteome.dc.affrc.go.jp/Soybean/.

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

Science.gov (United States)

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

Enhancement of Environmental Hazard Degradation in the Presence of Lignin: a Proteomics Study

OpenAIRE

Sun, Su; Xie, Shangxian; Cheng, Yanbing; Yu, Hongbo; Zhao, Honglu; Li, Muzi; Li, Xiaotong; Zhang, Xiaoyu; Yuan, Joshua S.; Dai, Susie Y.

2017-01-01

Proteomics studies of fungal systems have progressed dramatically based on the availability of more fungal genome sequences in recent years. Different proteomics strategies have been applied toward characterization of fungal proteome and revealed important gene functions and proteome dynamics. Presented here is the application of shot-gun proteomic technology to study the bio-remediation of environmental hazards by white-rot fungus. Lignin, a naturally abundant component of the plant biomass,...

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

Science.gov (United States)

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…

Advances in Proteomics of Mycobacterium leprae.

Science.gov (United States)

Parkash, O; Singh, B P

2012-04-01

Although Mycobacterium leprae was the first bacterial pathogen identified causing human disease, it remains one of the few that is non-cultivable. Understanding the biology of M. leprae is one of the primary challenges in current leprosy research. Genomics has been extremely valuable, nonetheless, functional proteins are ultimately responsible for controlling most aspects of cellular functions, which in turn could facilitate parasitizing the host. Furthermore, bacterial proteins provide targets for most of the vaccines and immunodiagnostic tools. Better understanding of the proteomics of M. leprae could also help in developing new drugs against M. leprae. During the past nearly 15 years, there have been several developments towards the identification of M. leprae proteins employing contemporary proteomics tools. In this review, we discuss the knowledge gained on the biology and pathogenesis of M. leprae from current proteomic studies. © 2012 The Authors. Scandinavian Journal of Immunology © 2012 Blackwell Publishing Ltd.

Insights into xanthomonas axonopodis pv. Citri biofilm through proteomics

KAUST Repository

Zimaro, Tamara

2013-08-07

quantitative real-time PCR and shown to consistently correlate with those deduced from the proteomic study. Conclusions: Differentially expressed proteins are enriched in functional categories. Firstly, proteins that are down-regulated in X. a. pv. Citri biofilms are enriched for the gene ontology (GO) terms \\'generation of precursor metabolites and energy\\' and secondly, the biofilm proteome mainly changes in \\'outer membrane and receptor or transport\\'. We argue that the differentially expressed proteins have a critical role in maintaining a functional external structure as well as enabling appropriate flow of nutrients and signals specific to the biofilm lifestyle. 2013 Zimaro et al.; licensee BioMed Central Ltd.

Proteomic classification of breast cancer.

LENUS (Irish Health Repository)

Kamel, Dalia

2012-11-01

Being a significant health problem that affects patients in various age groups, breast cancer has been extensively studied to date. Recently, molecular breast cancer classification has advanced significantly with the availability of genomic profiling technologies. Proteomic technologies have also advanced from traditional protein assays including enzyme-linked immunosorbent assay, immunoblotting and immunohistochemistry to more comprehensive approaches including mass spectrometry and reverse phase protein lysate arrays (RPPA). The purpose of this manuscript is to review the current protein markers that influence breast cancer prediction and prognosis and to focus on novel advances in proteomic classification of breast cancer.

MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes.

Science.gov (United States)

Zhang, Yanling; Zhang, Yong; Adachi, Jun; Olsen, Jesper V; Shi, Rong; de Souza, Gustavo; Pasini, Erica; Foster, Leonard J; Macek, Boris; Zougman, Alexandre; Kumar, Chanchal; Wisniewski, Jacek R; Jun, Wang; Mann, Matthias

2007-01-01

Mass spectrometry (MS)-based proteomics has become a powerful technology to map the protein composition of organelles, cell types and tissues. In our department, a large-scale effort to map these proteomes is complemented by the Max-Planck Unified (MAPU) proteome database. MAPU contains several body fluid proteomes; including plasma, urine, and cerebrospinal fluid. Cell lines have been mapped to a depth of several thousand proteins and the red blood cell proteome has also been analyzed in depth. The liver proteome is represented with 3200 proteins. By employing high resolution MS and stringent validation criteria, false positive identification rates in MAPU are lower than 1:1000. Thus MAPU datasets can serve as reference proteomes in biomarker discovery. MAPU contains the peptides identifying each protein, measured masses, scores and intensities and is freely available at http://www.mapuproteome.com using a clickable interface of cell or body parts. Proteome data can be queried across proteomes by protein name, accession number, sequence similarity, peptide sequence and annotation information. More than 4500 mouse and 2500 human proteins have already been identified in at least one proteome. Basic annotation information and links to other public databases are provided in MAPU and we plan to add further analysis tools.

MitoMiner: a data warehouse for mitochondrial proteomics data.

Science.gov (United States)

Smith, Anthony C; Blackshaw, James A; Robinson, Alan J

2012-01-01

MitoMiner (http://mitominer.mrc-mbu.cam.ac.uk/) is a data warehouse for the storage and analysis of mitochondrial proteomics data gathered from publications of mass spectrometry and green fluorescent protein tagging studies. In MitoMiner, these data are integrated with data from UniProt, Gene Ontology, Online Mendelian Inheritance in Man, HomoloGene, Kyoto Encyclopaedia of Genes and Genomes and PubMed. The latest release of MitoMiner stores proteomics data sets from 46 studies covering 11 different species from eumetazoa, viridiplantae, fungi and protista. MitoMiner is implemented by using the open source InterMine data warehouse system, which provides a user interface allowing users to upload data for analysis, personal accounts to store queries and results and enables queries of any data in the data model. MitoMiner also provides lists of proteins for use in analyses, including the new MitoMiner mitochondrial proteome reference sets that specify proteins with substantial experimental evidence for mitochondrial localization. As further mitochondrial proteomics data sets from normal and diseased tissue are published, MitoMiner can be used to characterize the variability of the mitochondrial proteome between tissues and investigate how changes in the proteome may contribute to mitochondrial dysfunction and mitochondrial-associated diseases such as cancer, neurodegenerative diseases, obesity, diabetes, heart failure and the ageing process.

Oil and gas prospects offshore Newfoundland: the Hibernia Project and opportunities for the Scottish industry

International Nuclear Information System (INIS)

Anon.

1992-01-01

The oil industry has been interested in prospects offshore Eastern Canada for well over a decade. In fact, the lack of substantial development activity has disappointed many in the industry. The offshore Canadian development of the Hibernia field could be the catalyst to spark world-wide interest and involvement in this newest of offshore petroleum provinces. The extent of the exploration of the field to date is reviewed, the prospects for development are assessed and the opportunities for Scottish industry in construction and development are examined. (author)

Proteomic analysis of the Arabidopsis thaliana-Botrytis cinerea ...

African Journals Online (AJOL)

A two-dimensional liquid chromatography (2D LC) system, ProteomeLab PF 2D, was employed to study the defence proteome of Arabidopsis following infection with the necrotrophic fungal pathogen, Botrytis cinerea. This system demonstrated differential protein expression in control and treated samples in some fractions.

Halobacterium salinarum NRC-1 PeptideAtlas: strategies for targeted proteomics

Science.gov (United States)

Van, Phu T.; Schmid, Amy K.; King, Nichole L.; Kaur, Amardeep; Pan, Min; Whitehead, Kenia; Koide, Tie; Facciotti, Marc T.; Goo, Young-Ah; Deutsch, Eric W.; Reiss, David J.; Mallick, Parag; Baliga, Nitin S.

2009-01-01

The relatively small numbers of proteins and fewer possible posttranslational modifications in microbes provides a unique opportunity to comprehensively characterize their dynamic proteomes. We have constructed a Peptide Atlas (PA) for 62.7% of the predicted proteome of the extremely halophilic archaeon Halobacterium salinarum NRC-1 by compiling approximately 636,000 tandem mass spectra from 497 mass spectrometry runs in 88 experiments. Analysis of the PA with respect to biophysical properties of constituent peptides, functional properties of parent proteins of detected peptides, and performance of different mass spectrometry approaches has helped highlight plausible strategies for improving proteome coverage and selecting signature peptides for targeted proteomics. Notably, discovery of a significant correlation between absolute abundances of mRNAs and proteins has helped identify low abundance of proteins as the major limitation in peptide detection. Furthermore we have discovered that iTRAQ labeling for quantitative proteomic analysis introduces a significant bias in peptide detection by mass spectrometry. Therefore, despite identifying at least one proteotypic peptide for almost all proteins in the PA, a context-dependent selection of proteotypic peptides appears to be the most effective approach for targeted proteomics. PMID:18652504

Top Down proteomics: Facts and perspectives

Energy Technology Data Exchange (ETDEWEB)

Catherman, Adam D.; Skinner, Owen S.; Kelleher, Neil L., E-mail: n-kelleher@northwestern.edu

2014-03-21

Highlights: • Top Down versus Bottom Up proteomics analysis. • Separations methods for Top Down proteomics. • Developments in mass spectrometry instrumentation and fragmentation. • Native mass spectrometry. - Abstract: The rise of the “Top Down” method in the field of mass spectrometry-based proteomics has ushered in a new age of promise and challenge for the characterization and identification of proteins. Injecting intact proteins into the mass spectrometer allows for better characterization of post-translational modifications and avoids several of the serious “inference” problems associated with peptide-based proteomics. However, successful implementation of a Top Down approach to endogenous or other biologically relevant samples often requires the use of one or more forms of separation prior to mass spectrometric analysis, which have only begun to mature for whole protein MS. Recent advances in instrumentation have been used in conjunction with new ion fragmentation using photons and electrons that allow for better (and often complete) protein characterization on cases simply not tractable even just a few years ago. Finally, the use of native electrospray mass spectrometry has shown great promise for the identification and characterization of whole protein complexes in the 100 kDa to 1 MDa regime, with prospects for complete compositional analysis for endogenous protein assemblies a viable goal over the coming few years.

Top Down proteomics: Facts and perspectives

International Nuclear Information System (INIS)

Catherman, Adam D.; Skinner, Owen S.; Kelleher, Neil L.

2014-01-01

Highlights: • Top Down versus Bottom Up proteomics analysis. • Separations methods for Top Down proteomics. • Developments in mass spectrometry instrumentation and fragmentation. • Native mass spectrometry. - Abstract: The rise of the “Top Down” method in the field of mass spectrometry-based proteomics has ushered in a new age of promise and challenge for the characterization and identification of proteins. Injecting intact proteins into the mass spectrometer allows for better characterization of post-translational modifications and avoids several of the serious “inference” problems associated with peptide-based proteomics. However, successful implementation of a Top Down approach to endogenous or other biologically relevant samples often requires the use of one or more forms of separation prior to mass spectrometric analysis, which have only begun to mature for whole protein MS. Recent advances in instrumentation have been used in conjunction with new ion fragmentation using photons and electrons that allow for better (and often complete) protein characterization on cases simply not tractable even just a few years ago. Finally, the use of native electrospray mass spectrometry has shown great promise for the identification and characterization of whole protein complexes in the 100 kDa to 1 MDa regime, with prospects for complete compositional analysis for endogenous protein assemblies a viable goal over the coming few years

Analytical performance of reciprocal isotope labeling of proteome digests for quantitative proteomics and its application for comparative studies of aerobic and anaerobic Escherichia coli proteomes

International Nuclear Information System (INIS)

Lo, Andy; Weiner, Joel H.; Li, Liang

2013-01-01

Graphical abstract: -- Highlights: •Investigating a strategy of reciprocal isotope labeling of comparative samples. •Filtering out incorrect peptide identification or quantification values. •Analyzing the proteome changes of E. coli cells grown aerobically or anaerobically. •Presenting guidelines for reciprocal labeling experimental design. -- Abstract: Due to limited sample amounts, instrument time considerations, and reagent costs, only a small number of replicate experiments are typically performed for quantitative proteome analyses. Generation of reproducible data that can be readily assessed for consistency within a small number of datasets is critical for accurate quantification. We report our investigation of a strategy using reciprocal isotope labeling of two comparative samples as a tool for determining proteome changes. Reciprocal labeling was evaluated to determine the internal consistency of quantified proteome changes from Escherichia coli grown under aerobic and anaerobic conditions. Qualitatively, the peptide overlap between replicate analyses of the same sample and reverse labeled samples were found to be within 8%. Quantitatively, reciprocal analyses showed only a slight increase in average overall inconsistency when compared with replicate analyses (1.29 vs. 1.24-fold difference). Most importantly, reverse labeling was successfully used to identify spurious values resulting from incorrect peptide identifications and poor peak fitting. After removal of 5% of the peptide data with low reproducibility, a total of 275 differentially expressed proteins (>1.50-fold difference) were consistently identified and were then subjected to bioinformatics analysis. General considerations and guidelines for reciprocal labeling experimental design and biological significance of obtained results are discussed

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

Science.gov (United States)

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.

The 3rd Central and Eastern European Proteomic Conference

Czech Academy of Sciences Publication Activity Database

Gadher, S. J.; Martinková, Jiřina; Drahoš, L.; Vékey, K.; Allmaier, G.; Kovářová, Hana

2010-01-01

Roč. 7, č. 1 (2010), s. 15-17 ISSN 1478-9450 Institutional research plan: CEZ:AV0Z50450515 Keywords : proteomics * proteome research * biomarkers Subject RIV: CE - Biochemistry Impact factor: 4.406, year: 2010

Tracking paraglacial sediment with cosmogenic 10Be using an example from the northwest Scottish Highlands

Science.gov (United States)

Fame, Michelle L.; Owen, Lewis A.; Spotila, James A.; Dortch, Jason M.; Caffee, Marc W.

2018-02-01

Beryllium-10 concentrations in samples of sediment and bedrock from five study sites across the Scottish Highlands trace paraglacial sediment sources and define the nature of glacial erosion for the late Quaternary. Exposure ages derived from 10Be concentrations in ridge and lower elevation bedrock range from 10 to 33 ka, which suggest that polythermal ice and warm based ice were primarily responsible for producing glacial sediment. Comparisons of 10Be concentrations between catchment-wide sediment (2.06 ± 0.34 × 104 to 11.24 ± 1.54 × 104 atoms g-1 SiO2; n = 33), near surface deposits (2.71 ± 0.33 × 104 to 3.48 ± 0.49 × 104 atoms g-1 SiO2; n = 6), 4-m-thick deep till (0.68 × 10410Be atoms g-1 SiO2; n = 1), ridge bedrock (8.93 ± 0.47 × 104 to 34.05 ± 1.66 × 104 atoms g-1 SiO2; n = 20), and lower elevation polished bedrock (6.74 ± 0.67 × 104 to 12.65 ± 0.7 × 104 atoms g-1 SiO2, n = 5) indicate that most sand fluxing through catchments in the Scottish Highlands is sourced from the remobilization and vertical mixing of near surface deposits. These findings indicate that glaciogenic material continues to dominate paraglacial sediment budgets more than 11 ka after deglaciation.

Cutting edge proteomics

DEFF Research Database (Denmark)

Bunkenborg, Jakob; Espadas, Guadalupe; Molina, Henrik

2013-01-01

Tryptic digestion is an important component of most proteomics experiments, and trypsin is available from many sources with a cost that varies by more than 1000-fold. This high-mass-accuracy LC-MS study benchmarks six commercially available trypsins with respect to autolytic species and sequence ...

7th February 2011 - Scottish Cabinet Secretary for Education and Lifelong Learning M. Russell MSP signing the guest book with Beams Department Head P. Collier and Adviser J. Ellis

CERN Multimedia

Maximilien Brice

2011-01-01

01-17:Scottish Cabinet Secretary for Education and Lifelong Learning M. Russell MSP signing the guest book with Beams Department Head P. Collier and Adviser J. Ellis 18-22: Teachers and Pupils signing the guest book 23-27: visiting the CERN control centre with P. Collier 28-32: visiting the LHCb underground area 33-74: visitng the ATLAS underground area Other members of the delegation: Chief Scientific Adviser to the Scottish Government and Chair in Molecular and Cell Biology at the University of Aberdeen A. Glover; Assistant Private Secretary M. Gallagher; Associate Director Institute for Gravitational Research, University of Glasgow J.Hough.

Proteomics of Rice Seed Germination

Directory of Open Access Journals (Sweden)

Dongli eHe

2013-07-01

Full Text Available Seed is a condensed form of plant. Under suitable environmental conditions, it can resume the metabolic activity from physiological quiescent status, and mobilize the reserves, biosynthesize new proteins, regenerate organelles and cell membrane, eventually protrude the radicle and enter into seedling establishment. So far, how these activities are regulated in a coordinated and sequential manner is largely unknown. With the availability of more and more genome sequence information and the development of mass spectrometry (MS technology, proteomics has been widely applied in analyzing the mechanisms of different biological processes, and proved to be very powerful. Regulation of rice seed germination is critical for rice cultivation. In recent years, a lot of proteomic studies have been conducted in exploring the gene expression regulation, reserves mobilization and metabolisms reactivation, which brings us new insights on the mechanisms of metabolism regulation during this process. Nevertheless, it also invokes a lot of questions. In this mini-review, we summarized the progress in the proteomic studies of rice seed germination. The current challenges and future perspectives were also discussed, which might be helpful for the following studies.

Proteomic identification of gender molecular markers in Bothrops jararaca venom.

Science.gov (United States)

Zelanis, André; Menezes, Milene C; Kitano, Eduardo S; Liberato, Tarcísio; Tashima, Alexandre K; Pinto, Antonio F M; Sherman, Nicholas E; Ho, Paulo L; Fox, Jay W; Serrano, Solange M T

2016-04-29

Variation in the snake venom proteome is a well-documented phenomenon; however, sex-based variation in the venom proteome/peptidome is poorly understood. Bothrops jararaca shows significant sexual size dimorphism and here we report a comparative proteomic/peptidomic analysis of venoms from male and female specimens and correlate it with the evaluation of important venom features. We demonstrate that adult male and female venoms have distinct profiles of proteolytic activity upon fibrinogen and gelatin. These differences were clearly reflected in their different profiles of SDS-PAGE, two-dimensional electrophoresis and glycosylated proteins. Identification of differential protein bands and spots between male or female venoms revealed gender-specific molecular markers. However, the proteome comparison by in-solution trypsin digestion and label-free quantification analysis showed that the overall profiles of male and female venoms are similar at the polypeptide chain level but show striking variation regarding their attached carbohydrate moieties. The analysis of the peptidomes of male and female venoms revealed different contents of peptides, while the bradykinin potentiating peptides (BPPs) showed rather similar profiles. Furthermore we confirmed the ubiquitous presence of four BPPs that lack the C-terminal Q-I-P-P sequence only in the female venom as gender molecular markers. As a result of these studies we demonstrate that the sexual size dimorphism is associated with differences in the venom proteome/peptidome in B. jararaca species. Moreover, gender-based variations contributed by different glycosylation levels in toxins impact venom complexity. Bothrops jararaca is primarily a nocturnal and generalist snake species, however, it exhibits a notable ontogenetic shift in diet and in venom proteome upon neonate to adult transition. As is common in the Bothrops genus, B. jararaca shows significant sexual dimorphism in snout-vent length and weight, with females being

Subnuclear proteomics in colorectal cancer

DEFF Research Database (Denmark)

Albrethsen, Jakob; Knol, Jaco C; Piersma, Sander R

2010-01-01

for early cancer detection. Here we evaluate a proteomics work flow for profiling protein constituents in subnuclear domains in colorectal cancer tissues and apply this work flow to a comparative analysis of the nuclear matrix fraction in colorectal adenoma and carcinoma tissue samples. First, we......Abnormalities in nuclear phenotype and chromosome structure are key features of cancer cells. Investigation of the protein determinants of nuclear subfractions in cancer may yield molecular insights into aberrant chromosome function and chromatin organization and in addition may yield biomarkers...... with statistics, we identified proteins that are significantly enriched in the nuclear matrix fraction relative to two earlier fractions (the chromatin-binding and intermediate filament fractions) isolated from six colorectal tissue samples. The total data set contained 2,059 non-redundant proteins. Gene ontology...

TAILS N-terminomic and proteomic datasets of healthy human dental pulp

Directory of Open Access Journals (Sweden)

Ulrich Eckhard

2015-12-01

Full Text Available The Data described here provide the in depth proteomic assessment of the human dental pulp proteome and N-terminome (Eckhard et al., 2015 [1]. A total of 9 human dental pulps were processed and analyzed by the positional proteomics technique TAILS (Terminal Amine Isotopic Labeling of Substrates N-terminomics. 38 liquid chromatography tandem mass spectrometry (LC-MS/MS datasets were collected and analyzed using four database search engines in combination with statistical downstream evaluation, to yield the by far largest proteomic and N-terminomic dataset of any dental tissue to date. The raw mass spectrometry data and the corresponding metadata have been deposited in ProteomeXchange with the PXD identifier ; Supplementary Tables described in this article are available via Mendeley Data (10.17632/555j3kk4sw.1.

Tyrosine-Nitrated Proteins: Proteomic and Bioanalytical Aspects.

Science.gov (United States)

Batthyány, Carlos; Bartesaghi, Silvina; Mastrogiovanni, Mauricio; Lima, Analía; Demicheli, Verónica; Radi, Rafael

2017-03-01

"Nitroproteomic" is under active development, as 3-nitrotyrosine in proteins constitutes a footprint left by the reactions of nitric oxide-derived oxidants that are usually associated to oxidative stress conditions. Moreover, protein tyrosine nitration can cause structural and functional changes, which may be of pathophysiological relevance for human disease conditions. Biological protein tyrosine nitration is a free radical process involving the intermediacy of tyrosyl radicals; in spite of being a nonenzymatic process, nitration is selectively directed toward a limited subset of tyrosine residues. Precise identification and quantitation of 3-nitrotyrosine in proteins has represented a "tour de force" for researchers. Recent Advances: A small number of proteins are preferential targets of nitration (usually less than 100 proteins per proteome), contrasting with the large number of proteins modified by other post-translational modifications such as phosphorylation, acetylation, and, notably, S-nitrosation. Proteomic approaches have revealed key features of tyrosine nitration both in vivo and in vitro, including selectivity, site specificity, and effects in protein structure and function. Identification of 3-nitrotyrosine-containing proteins and mapping nitrated residues is challenging, due to low abundance of this oxidative modification in biological samples and its unfriendly behavior in mass spectrometry (MS)-based technologies, that is, MALDI, electrospray ionization, and collision-induced dissociation. The use of (i) classical two-dimensional electrophoresis with immunochemical detection of nitrated proteins followed by protein ID by regular MS/MS in combination with (ii) immuno-enrichment of tyrosine-nitrated peptides and (iii) identification of nitrated peptides by a MIDAS™ experiment is arising as a potent methodology to unambiguously map and quantitate tyrosine-nitrated proteins in vivo. Antioxid. Redox Signal. 26, 313-328.

Childhood cognitive ability and incident dementia: the 1932 Scottish Mental Survey cohort into their tenth decade

OpenAIRE

Russ, T. C.; Hannah, J.; Batty, G. D.; Booth, C. C.; Deary, I. J.; Starr, J. M.

2017-01-01

BACKGROUND: The prevention of dementia is a global priority but its etiology is poorly understood. Early life cognitive ability has been linked to subsequent dementia risk but studies to date have been small and none has examined sex differences. METHODS: In the 1932 Scottish Mental Survey cohort, we related intelligence test scores at age 11 years in 16,370 boys and 16,097 girls (born in 1921) to incident dementia aged ≥65 years as ascertained using probabilistic linkage to electronic health...

Childhood cognitive ability and incident dementia: the 1932 Scottish Mental Survey cohort into their tenth decade

OpenAIRE

Russ, Tom C.; Hannah, Jean; Batty, G. David; Booth, Christopher C.; Deary, Ian J.; Starr, John M.

2017-01-01

Background: The prevention of dementia is a global priority but its aetiology is poorly understood. Early life cognitive ability has been linked to subsequent dementia risk but studies to date have been small and none has examined sex differences. Methods: In the 1932 Scottish Mental Survey cohort, we related intelligence test scores at age 11 years in 16,370 boys and 16,097 girls (born in 1921) to incident dementia aged ≥65 years as ascertained using probabilistic linkage to electronic healt...

PROTEINCHALLENGE: Crowd sourcing in proteomics analysis and software development

DEFF Research Database (Denmark)

Martin, Sarah F.; Falkenberg, Heiner; Dyrlund, Thomas Franck

2013-01-01

, including arguments for community-wide open source software development and “big data” compatible solutions for the future. For the meantime, we have laid out ten top tips for data processing. With these at hand, a first large-scale proteomics analysis hopefully becomes less daunting to navigate.......However there is clearly a real need for robust tools, standard operating procedures and general acceptance of best practises. Thus we submit to the proteomics community a call for a community-wide open set of proteomics analysis challenges—PROTEINCHALLENGE—that directly target and compare data analysis workflows......In large-scale proteomics studies there is a temptation, after months of experimental work, to plug resulting data into a convenient—if poorly implemented—set of tools, which may neither do the data justice nor help answer the scientific question. In this paper we have captured key concerns...

Differential proteomics study of platelets in asymptomatic constitutional macrothrombocytopenia: altered levels of cytoskeletal proteins.

Science.gov (United States)

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.

The value of chest X-ray in the Scottish Referral Guidelines for suspected head and neck cancer in 2144 patients.

Science.gov (United States)

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.

Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.

Science.gov (United States)

Deutsch, Eric W; Orchard, Sandra; Binz, Pierre-Alain; Bittremieux, Wout; Eisenacher, Martin; Hermjakob, Henning; Kawano, Shin; Lam, Henry; Mayer, Gerhard; Menschaert, Gerben; Perez-Riverol, Yasset; Salek, Reza M; Tabb, David L; Tenzer, Stefan; Vizcaíno, Juan Antonio; Walzer, Mathias; Jones, Andrew R

2017-12-01

The Proteomics Standards Initiative (PSI) of the Human Proteome Organization (HUPO) has now been developing and promoting open community standards and software tools in the field of proteomics for 15 years. Under the guidance of the chair, cochairs, and other leadership positions, the PSI working groups are tasked with the development and maintenance of community standards via special workshops and ongoing work. Among the existing ratified standards, the PSI working groups continue to update PSI-MI XML, MITAB, mzML, mzIdentML, mzQuantML, mzTab, and the MIAPE (Minimum Information About a Proteomics Experiment) guidelines with the advance of new technologies and techniques. Furthermore, new standards are currently either in the final stages of completion (proBed and proBAM for proteogenomics results as well as PEFF) or in early stages of design (a spectral library standard format, a universal spectrum identifier, the qcML quality control format, and the Protein Expression Interface (PROXI) web services Application Programming Interface). In this work we review the current status of all of these aspects of the PSI, describe synergies with other efforts such as the ProteomeXchange Consortium, the Human Proteome Project, and the metabolomics community, and provide a look at future directions of the PSI.

Investigating the Effect of Growth Phase on the Surface-Layer Associated Proteome of Lactobacillus acidophilus Using Quantitative Proteomics

Directory of Open Access Journals (Sweden)

Courtney Klotz

2017-11-01

Full Text Available Bacterial surface-layers (S-layers are semi-porous crystalline arrays that self-assemble to form the outermost layer of some cell envelopes. S-layers have been shown to act as scaffolding structures for the display of auxiliary proteins externally. These S-layer associated proteins have recently gained attention in probiotics due to their direct physical contact with the intestinal mucosa and potential role in cell proliferation, adhesion, and immunomodulation. A number of studies have attempted to catalog the S-layer associated proteome of Lactobacillus acidophilus NCFM under a single condition. However, due to the versatility of the cell surface, we chose to employ a multiplexing-based approach with the intention of accurately contrasting multiple conditions. In this study, a previously described lithium chloride isolation protocol was used to release proteins bound to the L. acidophilus S-layer during logarithmic and early stationary growth phases. Protein quantification values were obtained via TMT (tandem mass tag labeling combined with a triple-stage mass spectrometry (MS3 method. Results showed significant growth stage-dependent alterations to the surface-associated proteome while simultaneously highlighting the sensitivity and reproducibility of the technology. Thus, this study establishes a framework for quantifying condition-dependent changes to cell surface proteins that can easily be applied to other S-layer forming bacteria.

Stressor-induced proteome alterations in zebrafish: A meta-analysis of response patterns

Energy Technology Data Exchange (ETDEWEB)

Groh, Ksenia J., E-mail: ksenia.groh@eawag.ch [Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf (Switzerland); ETH Zürich, Swiss Federal Institute of Technology, Department of Chemistry and Applied Biosciences, 8093 Zürich (Switzerland); Suter, Marc J.-F. [Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf (Switzerland); ETH Zürich, Swiss Federal Institute of Technology, Department of Environmental Systems Science, 8092 Zürich (Switzerland)

2015-02-15

Highlights: • We compared reported proteome changes induced by various stressors in zebrafish. • Several proteins groups frequently responding to diverse stressors were identified. • These included energy metabolism enzymes, heat shock and cytoskeletal proteins. • Insufficient proteome coverage impedes identification of more specific responses. • Further research needs for proteomics in ecotoxicology are discussed. - Abstract: Proteomics approaches are being increasingly applied in ecotoxicology on the premise that the identification of specific protein expression changes in response to a particular chemical would allow elucidation of the underlying molecular pathways leading to an adverse effect. This in turn is expected to promote the development of focused testing strategies for specific groups of toxicants. Although both gel-based and gel-free global characterization techniques provide limited proteome coverage, the conclusions regarding the cellular processes affected are still being drawn based on the few changes detected. To investigate how specific the detected responses are, we analyzed a set of studies that characterized proteome alterations induced by various physiological, chemical and biological stressors in zebrafish, a popular model organism. Our analysis highlights several proteins and protein groups, including heat shock and oxidative stress defense proteins, energy metabolism enzymes and cytoskeletal proteins, to be most frequently identified as responding to diverse stressors. In contrast, other potentially more specifically responding protein groups are detected much less frequently. Thus, zebrafish proteome responses to stress reported by different studies appear to depend mostly on the level of stress rather than on the specific stressor itself. This suggests that the most broadly used current proteomics technologies do not provide sufficient proteome coverage to allow in-depth investigation of specific mechanisms of toxicant action

Stressor-induced proteome alterations in zebrafish: A meta-analysis of response patterns

International Nuclear Information System (INIS)

Groh, Ksenia J.; Suter, Marc J.-F.

2015-01-01

Highlights: • We compared reported proteome changes induced by various stressors in zebrafish. • Several proteins groups frequently responding to diverse stressors were identified. • These included energy metabolism enzymes, heat shock and cytoskeletal proteins. • Insufficient proteome coverage impedes identification of more specific responses. • Further research needs for proteomics in ecotoxicology are discussed. - Abstract: Proteomics approaches are being increasingly applied in ecotoxicology on the premise that the identification of specific protein expression changes in response to a particular chemical would allow elucidation of the underlying molecular pathways leading to an adverse effect. This in turn is expected to promote the development of focused testing strategies for specific groups of toxicants. Although both gel-based and gel-free global characterization techniques provide limited proteome coverage, the conclusions regarding the cellular processes affected are still being drawn based on the few changes detected. To investigate how specific the detected responses are, we analyzed a set of studies that characterized proteome alterations induced by various physiological, chemical and biological stressors in zebrafish, a popular model organism. Our analysis highlights several proteins and protein groups, including heat shock and oxidative stress defense proteins, energy metabolism enzymes and cytoskeletal proteins, to be most frequently identified as responding to diverse stressors. In contrast, other potentially more specifically responding protein groups are detected much less frequently. Thus, zebrafish proteome responses to stress reported by different studies appear to depend mostly on the level of stress rather than on the specific stressor itself. This suggests that the most broadly used current proteomics technologies do not provide sufficient proteome coverage to allow in-depth investigation of specific mechanisms of toxicant action

A high-quality catalog of the Drosophila melanogaster proteome

DEFF Research Database (Denmark)

Brunner, Erich; Ahrens, Christian H.; Mohanty, Sonaly

2007-01-01

% of the predicted Drosophila melanogaster proteome by detecting 9,124 proteins from 498,000 redundant and 72,281 distinct peptide identifications. This unprecedented high proteome coverage for a complex eukaryote was achieved by combining sample diversity, multidimensional biochemical fractionation and analysis...

Regional differences of the urinary proteomes in healthy Chinese individuals

OpenAIRE

Qin, Weiwei; Wu, Jianqiang; Pan, Li; Zhang, Fanshuang; Wang, Xiaorong; Zhang, Biao; Shan, Guangliang; Gao, Youhe

2017-01-01

Urine is a promising biomarker source for clinical proteomics studies. Although regional physiological differences are common in multi-center clinical studies, the presence of significant differences in the urinary proteomes of individuals from different regions remains unknown. In this study, morning urine samples were collected from healthy urban residents in three regions of China and urinary proteins were preserved using a membrane-based method (Urimem). The urine proteomes of 27 normal s...

Proteomic analyses of host and pathogen responses during bovine mastitis.

Science.gov (United States)

Boehmer, Jamie L

2011-12-01

The pursuit of biomarkers for use as clinical screening tools, measures for early detection, disease monitoring, and as a means for assessing therapeutic responses has steadily evolved in human and veterinary medicine over the past two decades. Concurrently, advances in mass spectrometry have markedly expanded proteomic capabilities for biomarker discovery. While initial mass spectrometric biomarker discovery endeavors focused primarily on the detection of modulated proteins in human tissues and fluids, recent efforts have shifted to include proteomic analyses of biological samples from food animal species. Mastitis continues to garner attention in veterinary research due mainly to affiliated financial losses and food safety concerns over antimicrobial use, but also because there are only a limited number of efficacious mastitis treatment options. Accordingly, comparative proteomic analyses of bovine milk have emerged in recent years. Efforts to prevent agricultural-related food-borne illness have likewise fueled an interest in the proteomic evaluation of several prominent strains of bacteria, including common mastitis pathogens. The interest in establishing biomarkers of the host and pathogen responses during bovine mastitis stems largely from the need to better characterize mechanisms of the disease, to identify reliable biomarkers for use as measures of early detection and drug efficacy, and to uncover potentially novel targets for the development of alternative therapeutics. The following review focuses primarily on comparative proteomic analyses conducted on healthy versus mastitic bovine milk. However, a comparison of the host defense proteome of human and bovine milk and the proteomic analysis of common veterinary pathogens are likewise introduced.

Plant plasma membrane proteomics for improving cold tolerance

Directory of Open Access Journals (Sweden)

Daisuke eTakahashi

2013-04-01

Full Text Available Plants are always exposed to various stresses. We have focused on freezing stress, which causes serious problems for agricultural management. When plants suffer freeze-induced damage, the plasma membrane is thought to be the primary site of injury because of its central role in regulation of various cellular processes. Cold tolerant species, however, adapt to such freezing conditions by modifying cellular components and functions (cold acclimation. One of the most important adaptation mechanisms to freezing is alteration of plasma membrane compositions and functions. Advanced proteomic technologies have succeeded in identification of many candidates that may play roles in adaptation of the plasma membrane to freezing stress. Proteomics results suggest that adaptations of plasma membrane functions to low temperature are associated with alterations of protein compositions during cold acclimation. Some of proteins identified by proteomic approaches have been verified their functional roles in freezing tolerance mechanisms further. Thus, accumulation of proteomic results in the plasma membrane is of importance for application to molecular breeding efforts to increase cold tolerance in crops.

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

Science.gov (United States)

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…