University of Turku

About: University of Turku is a education organization based out in Turku, Finland. It is known for research contribution in the topics: Population & Galaxy. The organization has 16296 authors who have published 45124 publications receiving 1505428 citations. The organization is also known as: Turun yliopisto & Åbo universitet.

Accuracy of protein flexibility predictions.

Abstract: Protein structural flexibility is important for catalysis, binding, and allostery. Flexibility has been predicted from amino acid sequence with a sliding window averaging technique and applied primarily to epitope search. New prediction parameters were derived from 92 refined protein structures in an unbiased selection of the Protein Data Bank by developing further the method of Karplus and Schulz (Naturwissenschaften 72:212-213, 1985). The accuracy of four flexibility prediction techniques was studied by comparing atomic temperature factors of known three-dimensional protein structures to predictions by using correlation coefficients. The size of the prediction window was optimized for each method. Predictions made with our new parameters, using an optimized window size of 9 residues in the prediction window, were giving the best results. The difference from another previously used technique was small, whereas two other methods were much poorer. Applicability of the predictions was also tested by searching for known epitopes from amino acid sequences. The best techniques predicted correctly 20 of 31 continuous epitopes in seven proteins. Flexibility parameters have previously been used for calculating protein average flexibility indices which are inversely correlated to protein stability. Indices with the new parameters showed better correlation to protein stability than those used previously; furthermore they had relationship even when the old parameters failed. (C) 1994 Wiley-Liss, Inc. (Less)

Collagenase-3 (MMP-13) is expressed by hypertrophic chondrocytes, periosteal cells, and osteoblasts during human fetal bone development.

Abstract: Collagenase-3 (MMP-13) is a novel matrix metalloproteinase, the expression of which has so far only been documented in human breast carcinomas and osteoarthritic cartilage. In this study we have examined the expression of MMP-13 during human fetal development. Northern blot hybridizations revealed abundant expression of MMP-13 mRNAs in total RNA from fetal cartilage and calvaria at gestational age of 15 weeks. By in situ hybridization MMP-13 transcripts were detected in chondrocytes of hypertrophic cartilage in vertebrae of the spinal column and in the dorsal end of ribs undergoing ossification, as well as in osteoblasts and periosteal cells below the inner periosteal region of ossified ribs. In contrast, no expression of MMP-13 could be detected in osteoclasts. Furthermore, expression of MMP-13 mRNA was detected in osteoblasts and fibroblasts primarily on the inner side of calvarial bone of the skull at 16 weeks of gestation. Expression of MMP-13 mRNA by primary human fetal chondrocytes in culture was enhanced by transforming growth factor-beta (TGF-beta) and inhibited by bone morphogenetic protein-2 (BMP-2). No expression of MMP-13 mRNA could be noted in other fetal tissues, including the skin, lungs, neural tissue, muscle, and liver. These results suggest that MMP-13 plays an important role in the extracellular matrix remodeling during fetal bone development both via endochondral and intramembranous ossification.

Anti-bullying intervention: implementation and outcome.

Abstract: BACKGROUND: The participant role approach represents a view of bullying as a group process in which bystanders often encourage the bullying or silently witness it, while little support is given to the victim (e.g. Salmivalli, Lagerspetz, Bjarkqvist, Osterman, & Kaukiainen, 1996). There is a discrepancy between students' attitudes (which are often against bullying) and their actual behaviour in bullying situations, and this may be an important factor contributing to the persistence of the problem. AIM: The aim of the present study was to evaluate the effects of an anti-bullying intervention programme targeting the group as a whole. Class teachers who attended a 1-year training course carried out the interventions in school classes. The present evaluation of the project is based on multi-level modelling, assessing the programme effects after 12 months of intervention, utilizing a cohort longitudinal design with adjacent cohorts (Olweus & Alsaker, 1991) also taking into account the degree of implementation of the programme. SAMPLE: The intervention was implemented in 48 school classes (Grades 4, 5, and 6) from 16 Finnish schools, involving 1,220 children (600 girls and 620 boys). METHOD: The present report is based on questionnaire data collected at two assessment points during the project, assessing the frequencies of bullies and victims, the extent of observed and experienced bullying, students' attitudes and efficacy beliefs related to bullying, and their participant role behaviours (self- and peer-reported). Reports were collected from teachers about the concrete actions taken in order to compare the actual content of the intervention to what had been planned. RESULTS: A positive impact of the intervention programme was found on several outcome variables (e.g. frequencies of bullies and victims, observed and experienced bullying, attitudes and efficacy beliefs, and to some extent, participant role behaviours). The intervention effects were found more often in Grade 4 than in Grade 5, and often only in schools with a high degree of implementation of the programme.

Analyzing or explaining beta diversity? Understanding the targets of different methods of analysis.

Abstract: It has been actively discussed recently what statistical methods are appropriate when one is interested in testing hypotheses about the origin of beta diversity, especially whether one should use the raw-data approach (e.g., canonical analysis such as RDA and CCA) or the distance approach (e.g., Mantel test and multiple regression on distance matrices). Most of the confusion seems to stem from uncertainty as to what is the response variable in the different approaches. Here our aim is to clarify this issue. We also show that, although both the raw-data approach and the distance approach can often be used to address the same ecological hypothesis, they target fundamentally different predictions of those hypotheses. As the two approaches shed light on different aspects of the ecological hypotheses, they should be viewed as complementary rather than alternative ways of analyzing data. However, in some cases only one of the approaches may be appropriate. We argue that S. P. Hubbell's neutral theory can only be tested using the distance approach, because its testable predictions are stated in terms of distances, not in terms of raw data. In all cases, the decision on which method is chosen must be based on which addresses the question at hand, it cannot be based on which provides the highest proportion of explained variance in simulation studies.