2DDB – a bioinformatics solution for analysis of quantitative proteomics data

BACKGROUND: We present 2DDB, a bioinformatics solution for storage, integration and analysis of quantitative proteomics data. As the data complexity and the rate with which it is produced increases in the proteomics field, the need for flexible analysis software increases. RESULTS: 2DDB is based on a core data model describing fundamentals such as experiment description and identified proteins. The extended data models are built on top of the core data model to capture more specific aspects of the data. A number of public databases and bioinformatical tools have been integrated giving the user access to large amounts of relevant data. A statistical and graphical package, R, is used for statistical and graphical analysis. The current implementation handles quantitative data from 2D gel electrophoresis and multidimensional liquid chromatography/mass spectrometry experiments. CONCLUSION: The software has successfully been employed in a number of projects ranging from quantitative liquid-chromatography-mass spectrometry based analysis of transforming growth factor-beta stimulated fi-broblasts to 2D gel electrophoresis/mass spectrometry analysis of biopsies from human cervix. The software is available for download at SourceForge

Reduction of physiological stress by urban green space in a multisensory virtual experiment

Although stress is an increasing global health problem in cities, urban green spaces can provide health benefits. There is, however, a lack of understanding of the link between physiological mechanisms and qualities of urban green spaces. Here, we compare the effects of visual stimuli (360 degree virtual photos of an urban environment, forest, and park) to the effects of congruent olfactory stimuli (nature and city odours) and auditory stimuli (bird songs and noise) on physiological stress recovery. Participants (N = 154) were pseudo-randomised into participating in one of the three environments and subsequently exposed to stress (operationalised by skin conductance levels). The park and forest, but not the urban area, provided significant stress reduction. High pleasantness ratings of the environment were linked to low physiological stress responses for olfactory and to some extent for auditory, but not for visual stimuli. This result indicates that olfactory stimuli may be better at facilitating stress reduction than visual stimuli. Currently, urban planners prioritise visual stimuli when planning open green spaces, but urban planners should also consider multisensory qualities

Sounds of Nature in the City: No Evidence of Bird Song Improving Stress Recovery

Noise from city traffic is one of the most significant environmental stressors. Natural soundscapes, such as bird songs, have been suggested to potentially mitigate or mask noise. All previous studies on masking noise use self-evaluation data rather than physiological data. In this study, while respondents (n = 117) watched a 360\ub0 virtual reality (VR) photograph of a park, they were exposed to different soundscapes and mild electrical shocks. The soundscapes-"bird song", "bird song and traffic noise", and "traffic noise"-were played during a 10 min recovery period while their skin conductance levels were assessed as a measure of arousal/stress. No significant difference in stress recovery was found between the soundscapes although a tendency for less stress in "bird song" and more stress in "traffic noise" was noted. All three soundscapes, however, significantly reduced stress. This result could be attributed to the stress-reducing effect of the visual VR environment, to the noise levels being higher than 47 dBA (a level known to make masking ineffective), or to the respondents finding bird songs stressful. Reduction of stress in cities using masking with natural sounds requires further studies with not only larger samples but also sufficient methods to detect potential sex differences

REST suppression mediates neural conversion of adult human fibroblasts via microRNA-dependent and -independent pathways.

Direct conversion of human fibroblasts into mature and functional neurons, termed induced neurons (iNs), was achieved for the first time 6 years ago. This technology offers a promising shortcut for obtaining patient- and disease-specific neurons for disease modeling, drug screening, and other biomedical applications. However, fibroblasts from adult donors do not reprogram as easily as fetal donors, and no current reprogramming approach is sufficiently efficient to allow the use of this technology using patient-derived material for large-scale applications. Here, we investigate the difference in reprogramming requirements between fetal and adult human fibroblasts and identify REST as a major reprogramming barrier in adult fibroblasts. Via functional experiments where we overexpress and knockdown the REST-controlled neuron-specific microRNAs miR-9 and miR-124, we show that the effect of REST inhibition is only partially mediated via microRNA up-regulation. Transcriptional analysis confirmed that REST knockdown activates an overlapping subset of neuronal genes as microRNA overexpression and also a distinct set of neuronal genes that are not activated via microRNA overexpression. Based on this, we developed an optimized one-step method to efficiently reprogram dermal fibroblasts from elderly individuals using a single-vector system and demonstrate that it is possible to obtain iNs of high yield and purity from aged individuals with a range of familial and sporadic neurodegenerative disorders including Parkinson's, Huntington's, as well as Alzheimer's disease

Mild-to-Moderate Kidney Dysfunction and Cardiovascular Disease: Observational and Mendelian Randomization Analyses

BACKGROUND: End-stage renal disease is associated with a high risk of cardiovascular events. It is unknown, however, whether mild-to-moderate kidney dysfunction is causally related to coronary heart disease (CHD) and stroke. METHODS: Observational analyses were conducted using individual-level data from 4 population data sources (Emerging Risk Factors Collaboration, EPIC-CVD [European Prospective Investigation into Cancer and Nutrition-Cardiovascular Disease Study], Million Veteran Program, and UK Biobank), comprising 648 135 participants with no history of cardiovascular disease or diabetes at baseline, yielding 42 858 and 15 693 incident CHD and stroke events, respectively, during 6.8 million personyears of follow-up. Using a genetic risk score of 218 variants for estimated glomerular filtration rate (eGFR), we conducted Mendelian randomization analyses involving 413 718 participants (25917 CHD and 8622 strokes) in EPIC-CVD, Million Veteran Program, and UK Biobank. RESULTS: There were U-shaped observational associations of creatinine-based eGFR with CHD and stroke, with higher risk in participants with eG FR values 105 mL.min(-1).1.73 m(-2), compared with those with eG FR between 60 and 105 mL.min(-1).1.73 m(-2). Mendelian randomization analyses for CHD showed an association among participants with eGFR 105 mL.min(-1).1.73 m(-2). Results were not materially different after adjustment for factors associated with the eGFR genetic risk score, such as lipoprotein(a), triglycerides, hemoglobin Alc, and blood pressure. Mendelian randomization results for stroke were nonsignificant but broadly similar to those for CHD. CONCLUSIONS: In people without manifest cardiovascular disease or diabetes, mild-to-moderate kidney dysfunction is causally related to risk of CHD, highlighting the potential value of preventive approaches that preserve and modulate kidney function

World Health Organization cardiovascular disease risk charts: revised models to estimate risk in 21 global regions

BACKGROUND: To help adapt cardiovascular disease risk prediction approaches to low-income and middle-income countries, WHO has convened an effort to develop, evaluate, and illustrate revised risk models. Here, we report the derivation, validation, and illustration of the revised WHO cardiovascular disease risk prediction charts that have been adapted to the circumstances of 21 global regions. METHODS: In this model revision initiative, we derived 10-year risk prediction models for fatal and non-fatal cardiovascular disease (ie, myocardial infarction and stroke) using individual participant data from the Emerging Risk Factors Collaboration. Models included information on age, smoking status, systolic blood pressure, history of diabetes, and total cholesterol. For derivation, we included participants aged 40-80 years without a known baseline history of cardiovascular disease, who were followed up until the first myocardial infarction, fatal coronary heart disease, or stroke event. We recalibrated models using age-specific and sex-specific incidences and risk factor values available from 21 global regions. For external validation, we analysed individual participant data from studies distinct from those used in model derivation. We illustrated models by analysing data on a further 123 743 individuals from surveys in 79 countries collected with the WHO STEPwise Approach to Surveillance. FINDINGS: Our risk model derivation involved 376 177 individuals from 85 cohorts, and 19 333 incident cardiovascular events recorded during 10 years of follow-up. The derived risk prediction models discriminated well in external validation cohorts (19 cohorts, 1 096 061 individuals, 25 950 cardiovascular disease events), with Harrell's C indices ranging from 0·685 (95% CI 0·629-0·741) to 0·833 (0·783-0·882). For a given risk factor profile, we found substantial variation across global regions in the estimated 10-year predicted risk. For example, estimated cardiovascular disease risk for a 60-year-old male smoker without diabetes and with systolic blood pressure of 140 mm Hg and total cholesterol of 5 mmol/L ranged from 11% in Andean Latin America to 30% in central Asia. When applied to data from 79 countries (mostly low-income and middle-income countries), the proportion of individuals aged 40-64 years estimated to be at greater than 20% risk ranged from less than 1% in Uganda to more than 16% in Egypt. INTERPRETATION: We have derived, calibrated, and validated new WHO risk prediction models to estimate cardiovascular disease risk in 21 Global Burden of Disease regions. The widespread use of these models could enhance the accuracy, practicability, and sustainability of efforts to reduce the burden of cardiovascular disease worldwide. FUNDING: World Health Organization, British Heart Foundation (BHF), BHF Cambridge Centre for Research Excellence, UK Medical Research Council, and National Institute for Health Research

IAS 41 - Värdering av skog

Införandet av standarden IAS/IFRS i Sverige är en effekt av den internationalisering som skett de senaste åren. En stor skillnad märks bland de företag som nu måste redovisa tillgångar till verkliga värden istället för som tidigare till historiska värden. Skogskoncernerna ställs inför ett sådant faktum. Effekten blir att en mer rättvisande bild av skogens värde uppkommer. De intervjuade företagen, Bergvik Skog AB, Holmen, SCA, Sveaskog och Öhrlings PricewaterhouseCoopers håller med om att dolda värden försvinner och en mer rättvisande bild uppkommer men anser även att IAS 41 inte är direkt anpassat för nordiskt skogsbruk och att endast en approximation av det verkliga värdet kan uppnås. Respondenterna åsyftar särskilt på de lagstadgade återplanteringskostnader som inte får vara med i beräkningarna enligt en bokstavstolkning av IAS 41 men som ändå tas med av svenska skogsbolag. IAS 41 förespråkar främst att skogstillgångarna ska värderas enligt rådande marknadspriser. Då det saknas transaktioner av skogsmark i de storlekar våra respondenter har blir följden att marknadspris inte kan tillämpas. Företagen får därför använda sig av en alternativregel, nuvärdesberäkningen. Denna baseras på att de närmaste 100 årens kassaflöden diskonteras tillbaka till nutid med en diskonteringsränta som för samtliga företag i uppsatsen visade sig vara 6,25 %. Uppsatsens arbete startades med att den teori som finns inom området samlades in och senare ställdes mot de telefonintervjuer som vi genomförde. Analysen ställer således empirin mot teorin och leder till en slutsats. Vår uppsats visar att IAS 41 inte är fullt tillämpad för svenskt skogsbruk men att den ändå fungerar tillfredställande om inte en bokstavstolkning av standarden efterlevs.The implementation of IAS/IFRS in Sweden is an outcome of the internationalization which has occurred in the past years. A huge difference can be noticed among the companies that now have to draw account using a fair value instead of earlier historical costs. The forest product companies are the ones facing this change. The effect of this is that a more true and fair view on the forest assets can be achieved. The interviewed companies in our essay, Bergvik Skog AB, Holmen, SCA, Sveaskog and Öhrlings PricewaterhouseCoopers all agree that the hidden value disappears and that a more true and fair value appears when dealing with IAS 41. Moreover, it is their opinion that the standard is not suited for the Nordic agriculture and the fair value is only an approximation. They especially refer this to the restoration costs, set by law in Sweden, which according to IAS 41 literally not can be included in the calculations. IAS 41 says that the quoted market price should be used as a first option for calculating the fair value. However, because there are no markets in the Swedish forest sector that accurately measure the sizes of the companies forest assets, market values can not be used to give a fair value. This is why the companies have to use the alternative rule, calculating the present value of expected net cash flows. The calculation is based on 100 year cash flows that is discounted back to today with a discount rate witch appeared to be 6,35% in all of the included companies in our essay. The essay started with collecting the available theory on our topic and witch we later tested on our empirical interviews. This then resulted in a conclusion. Our findings in this study is that IAS 41 not suited for Swedish forest companies, but it works if they don’t apply the standard literally

Hur reagerar de fyra stora?

Bakgrund och problem: För att kunna uppfylla syftet med revisionen är det nödvändigt att revisorn är oberoende. Den reglering som finns gällande oberoendet har diskuterats under en lång tid och på senare år har flera förändringar skett, framförallt internationellt sett. Även i Sverige är förändringar på gång och i maj 2006 antog riksdagen ett förslag från regeringen som träder ikraft den 1 januari 2007. Den nya lagen innebär att en revisionsbyrå inte längre får ge yrkesmässigt biträde vid bokföringen till ett större företag om samma byrå även tillhandahåller revisionen till företaget. Detta kan medföra att revisionsbyråerna kan tvingas göra sig av med konsultations eller revisionsuppdrag. Syfte: Att undersöka vilken påverkan de skärpta jävsreglerna har på revisorsbyråerna samt klargöra hur de nya reglerna kommer att påverka oberoendet. Vi avser även att undersöka om det finns några uttalade strategier för hur revisionsbyråerna ska bemöta reglerna. Avgränsningar: Uppsatsen undersöker enbart vilken påverkan de nya reglerna har på revisionsbyråerna och inte hur de påverkar mottagarna av tjänsterna. Endast revisionsbyråer i Göteborg kommer att undersökas på grund av kostnads och tidsskäl. Metod: Uppsatsen har en kvalitativ ansats. Intervjuer har genomförts med revisorer från de fyra stora revisionsbyråerna. Byråerna fick svara på frågor om påverkan, oberoendet och vilka eventuella strategier de har för att bemöta reglerna. Empirin har analyserats med hjälp av den framtagna referensramen och är inriktad på att urskilja eventuella likheter och skillnader mellan respondenternas svar. Vi har försökt att besvara varför dessa uppkommer. Resultat och slutsatser: De nya reglerna får en liten påverkan på revisionsbyråerna då de har få kombiuppdrag inom den träffade kategorin företag. Av denna anledning finns inte några utarbetade aktiva strategier framtagna. Det faktiska oberoendet får inte någon förändring utan det som förbättras är det synliga oberoendet till ett pris av längre tidsåtgång. Förslag till fortsatt forskning: Det vore intressant att i framtiden undersöka de verkliga effekterna av de nya reglerna och inte bara tänkbara scenarion. Även hur mottagarna av revisionen påverkas skulle vara intressant. En ytterliggare aspekt att undersöka är om det finns skillnader för påverkan på olika slags orter

Proteomics - the protein expression technology to study connective tissue biology

During the formation of peribronchial fibrosis in asthma, remodeling of connective tissue is due to an increase in deposition of extracellular matrix components like that of specific types of collagens and proteoglycans. By taking bronchial biopsies, we were able to isolate cell cultures derived from asthmatic patients and healthy volunteers, which provides a good model system to study differences regarding cell morphology and key connective tissue proteins in the remodeling process. Proteomics, utilizing two-dimensional electrophoresis and modern image analysis systems have made it possible to study protein expression and regulation of proteins in biological systems. By using this powerful tool, it is possible to quantitatively study protein regulation and to obtain increased knowledge about the mechanism behind the inflammatory process and formation of peribronchial fibrosis. We have optimized a proteomic protocol enabling detailed investigation of the protein expression pattern in human lung cells. An increased expression pattern was obtained, whereby 20 protein spots could be detected by image analysis in the stimulation. These proteins are correlated to the transformation of normal fibroblasts to myofibroblasts which are involved in the remodeling processes observed in asthma

Biglycan isoforms with differences in polysaccharide substitution and core protein in human lung fibroblasts.

Biglycan is widely distributed in the extracellular matrix and is a member of the small proteoglycan family characterized by a core protein with leucine-rich repeat motifs. We show in this paper for the first time that biglycan from human lung fibroblasts can be expressed as different isoforms. These isoforms can be separated from the predominant form of biglycan by hydrophobic interaction chromatography, where the more hydrophobic isoforms are retarded. The newly found isoforms of biglycan have a smaller core protein substituted with smaller glycosaminoglycan chains, migrating on SDS/PAGE at between 110 and 200 kDa. These molecules were identified as biglycan using MALDI-TOF MS. Identification of C-terminal peptides together with glycosylation of the N-terminal glycosaminoglycan sites excludes the possibility of terminal proteolytic cleavage. The biglycan isoforms are N-glycosylated, which demonstrates that a lack in N-glycosylation is not the reason for a smaller core. Two components revealed by RT-PCR indicate alternative splicing, which could be located in regions of the protein that have not been identified, with the exclusion of sites of glycosylations. Analyses of glycosaminoglycan chain length of the isoforms show that besides the normally occurring glycosaminoglycan chains, there is a mixture of shorter glycosaminoglycan chains. Structural analysis shows that these glycosaminoglycan chains contain a lower proportion of iduronic acid (61%) relative to glucuronic acid when compared to the glycosaminoglycan chain of the predominant form of biglycan (71%). We can anticipate that variation in structure of biglycan can cause changes in the connective tissue formation depending on its ability to bind matrix molecules, as well as cytokines