The Critical Role of N- and C-Terminal Contact in Protein Stability and Folding of a Family 10 Xylanase under Extreme Conditions

Background: Stabilization strategies adopted by proteins under extreme conditions are very complex and involve various kinds of interactions. Recent studies have shown that a large proportion of proteins have their N- and C-terminal elements in close contact and suggested they play a role in protein folding and stability. However, the biological significance of this contact remains elusive. Methodology: In the present study, we investigate the role of N- and C-terminal residue interaction using a family 10 xylanase (BSX) with a TIM-barrel structure that shows stability under high temperature,alkali pH, and protease and SDS treatment. Based on crystal structure,an aromatic cluster was identified that involves Phe4, Trp6 and Tyr343 holding the Nand C-terminus together; this is a unique and important feature of this protein that might be crucial for folding and stabilityunder poly-extreme conditions. Conclusion: A series of mutants was created to disrupt this aromatic cluster formation and study the loss of stability and function under given conditions. While the deletions of Phe4 resulted in loss of stability, removal of Trp6 and Tyr343 affected in vivo folding and activity. Alanine substitution with Phe4, Trp6 and Tyr343 drastically decreased stability under all parameters studied. Importantly,substitution of Phe4 with Trp increased stability in SDS treatment.Mass spectrometry results of limited proteolysis further demonstrated that the Arg344 residue is highly susceptible to trypsin digestion in sensitive mutants such as DF4, W6A and Y343A, suggesting again that disruption of the Phe4-Trp6-Tyr343 (F-W-Y) cluster destabilizes the N-and C-terminal interaction. Our results underscore the importance of N- and C-terminal contact through aromatic interactions in protein folding and stability under extreme conditions, and these results may be useful to improve the stability of other proteins under suboptimal conditions.

A course for teaching design research methodology

Design research informs and supports practice by developing knowledge to improve the chances of producing successful products.Training in design research has been poorly supported. Design research uses human and natural/technical sciences, embracing all facets of design; its methods and tools are adapted from both these traditions. However, design researchers are rarely trained in methods from both the traditions. Research in traditional sciences focuses primarily on understanding phenomena related to human, natural, or technical systems. Design research focuses on supporting improvement of such systems, using understanding as a necessary but not sufficient step, and it must embrace methods for both understanding reality and developing support for its improvement. A one-semester, postgraduate-level, credited course that has been offered since 2002, entitled Methodology for Design Research, is described that teaches a methodology for carrying out research into design. Its steps are to clarify research success; to understand relevant phenomena of design and how these influence success; to use this to envision design improvement and develop proposals for supporting improvement; to evaluate support for its influence on success; and, if unacceptable, to modify, support, or improve the understanding of success and its links to the phenomena of design. This paper highlights some major issues about the status of design research and describes how design research methodology addresses these. The teaching material, model of delivery, and evaluation of the course on methodology for design research are discussed.

Invariant-preserving Petri net reduction and conditions for invariant-existence

The use of invariants is an important tool for analysis of distributed and concurrent systems modeled by Petri nets. For a large practical system, the computation of desired invariants by the existing techniques is a time-consuming task. This paper proposes a theoretical foundation for simplified computation of desired invariants. We provide invariant-preserving Petri net reduction rules followed by the conditions for the existence of invariants in various well-structured nets. If an invariant exists, it can be found directly from the net structure using the formulas derived, or by applying the existing techniques on the reduced net.

Foaming of slags under dynamic conditions

Slag foaming under dynamic conditions has been studied in laboratory scale to examine the influence of properties commonly used to describe the foaminess and foam stability of slags under steady-state conditions. Synthetically produced slags with compositions relevant to tool steel and stainless steel production were studied through X-ray equipment in measurements simulating the dynamic conditions found in real processes. It is found that the dynamic systems display a more complex behavior than systems Under steady state. Traditional theories for foaming do not seem to be valid for slag foaming under dynamic conditions. The foam displays a fluctuating behavior, which the presently available models are not able to take into account. The concept of a foaming index does not seem to be applicable, resulting in the need for alternative models.

The fluctuations in slag foam under dynamic conditions

In the present article, slag foaming phenomenon under dynamic conditions is critically analyzed on the basis of the results of high-temperature X-ray image analysis experiments. The results indicate that the mismatch between the gas generation rate and gas escape rate has a serious impact on the foam height. This mismatch is attributed to the chemical reaction rate, which has to be considered in modeling slag foaming under dynamic conditions. The results further imply that a critical ratio of bubble size/crucible size exists, where wall effects are likely to become prominent.

Drop formation in non-newtonian liquids under pulsed conditions

Drop formation from single nozzles under pulsed flow conditions in non-Newtonian fluids following the power law model has been studied. An existing model has been modified to explain the experimental data. The flow conditions employed correspond to the mixer—settler type of operation in pulsed sieve-plate extraction columns. The modified model predicts the drop sizes satisfactorily. It has been found that consideration of non-Newtonian behaviour is important at low pulse intensities and its significance decreases with increasing intensity of pulsation. Further, the proposed model for single orifices has been tested to predict the sizes of drops formed from a sieve-plate distributor having four holes, and has been found to predict the sizes fairly well in the absence of coalescence.

Subject Teacher Training and Teaching in English

The purpose of this Master s thesis is on one hand to find out how CLIL (Content and Language Integrated Learning) teachers and English teachers perceive English and its use in teaching, and on the other hand, what they consider important in subject teacher education in English that is being planned and piloted in STEP Project at the University of Helsinki Department of Teacher Education. One research question is also what kind of language requirements teachers think CLIL teachers should have. The research results are viewed in light of previous research and literature on CLIL education. Six teachers participate in this study. Two of them are English teachers in the comprehensive school, two are class teachers in bilingual elementary education, and two are subject teachers in bilingual education, one of whom teaches in a lower secondary school and the other in an upper secondary school. One English teacher and one bilingual class teacher have graduated from a pilot class teacher program in English that started at the University of Helsinki in the middle of the 1990 s. The bilingual subject teachers are not trained in English but they have learned English elsewhere, which is a particular focus of interest in this study because it is expected that a great number of CLIL teachers in Finland do not have actual studies in English philology. The research method is interview and this is a qualitative case study. The interviews are recorded and transcribed for the ease of analysis. The English teachers do not always use English in their lessons and they would not feel confident in teaching another subject completely in English. All of the CLIL teachers trust their English skills in teaching, but the bilingual class teachers also use Finnish during lessons either because some teaching material is in Finnish, or they feel that rules and instructions are understood better in mother tongue or students English skills are not strong enough. One of the bilingual subject teachers is the only one who consciously uses only English in teaching and in discussions with students. Although teachers good English skills are generally considered important, only the teachers who have graduated from the class teacher education in English consider it important that CLIL teachers would have studies in English philology. Regarding the subject teacher education program in English, the respondents hope that its teachers will have strong enough English skills and that it will deliver what it promises. Having student teachers of different subjects studying together is considered beneficial. The results of the study show that acquiring teaching material in English continues to be the teachers own responsibility and a huge burden for the teachers, and there has, in fact, not been much progress in the matter since the beginning of CLIL education. The bilingual subject teachers think, however, that using one s own material can give new inspiration to teaching and enable the use of various pedagogical methods. Although it is questionable if the language competence requirements set for CLIL teachers by the Finnish Ministry of Education are not adhered to, it becomes apparent in the study that studies in English philology do not necessarily guarantee strong enough language skills for CLIL teaching, but teachers own personality and self-confidence have significance. Keywords: CLIL, bilingual education, English, subject teacher training, subject teacher education in English, STEP

In situ surface modification of molybdenum-doped organic-inorganic hybrid TiO2 nanoparticles under hydrothermal conditions and treatment of pharmaceutical effluent

Molybdenum-doped TiO2 organic-inorganic hybrid nanoparticles were synthesized under mild hydrothermal conditions by in situ surface modification using n-butylamine. This was carried out at 150 degrees C at autogeneous pressure over 18 h. n-Butylamine was selected as a surfactant since it produced nanoparticles of the desired size and shape. The products were characterized using powder X-ray diffraction, Fourier transform infrared spectrometry, dynamic light-scattering spectroscopy, UV-Vis spectroscopy and transmission electron microscopy. Chemical oxygen demand was estimated in order to determine the photodegradation efficiency of the molybdenum-doped TiO2 hybrid nanoparticles in the treatment of pharmaceutical effluents. It was found that molybdenum-doped TiO2 hybrid nanoparticles showed higher photocatalytic efficiency than untreated TiO2 nanoparticles.

On the use of weather radar for mesoscale applications in northern conditions

Mesoscale weather phenomena, such as the sea breeze circulation or lake effect snow bands, are typically too large to be observed at one point, yet too small to be caught in a traditional network of weather stations. Hence, the weather radar is one of the best tools for observing, analyzing and understanding their behavior and development. A weather radar network is a complex system, which has many structural and technical features to be tuned, from the location of each radar to the number of pulses averaged in the signal processing. These design parameters have no universal optimal values, but their selection depends on the nature of the weather phenomena to be monitored as well as on the applications for which the data will be used. The priorities and critical values are different for forest fire forecasting, aviation weather service or the planning of snow ploughing, to name a few radar-based applications. The main objective of the work performed within this thesis has been to combine knowledge of technical properties of the radar systems and our understanding of weather conditions in order to produce better applications able to efficiently support decision making in service duties for modern society related to weather and safety in northern conditions. When a new application is developed, it must be tested against ground truth . Two new verification approaches for radar-based hail estimates are introduced in this thesis. For mesoscale applications, finding the representative reference can be challenging since these phenomena are by definition difficult to catch with surface observations. Hence, almost any valuable information, which can be distilled from unconventional data sources such as newspapers and holiday shots is welcome. However, as important as getting data is to obtain estimates of data quality, and to judge to what extent the two disparate information sources can be compared. The presented new applications do not rely on radar data alone, but ingest information from auxiliary sources such as temperature fields. The author concludes that in the future the radar will continue to be a key source of data and information especially when used together in an effective way with other meteorological data.

Effect of soil preparation of boreal spruce forest on air and soil temperature conditions in forest regeneration areas.

The effect of scarification, ploughing and cross-directional plouhing on temperature conditions in the soil and adjacent air layer have been studied during 11 consecutive growth periods by using an unprepared clear-cut area as a control site. The maximum and minimum temperatures were measured daily in the summer months, and other temperature observations were made at four-hour intervals by means of a Grant measuring instrument. The development of the seedling stand was also followed in order to determine its shading effect on the soil surface. Soil preparation decreased the daily temperature amplitude of the air at the height of 10 cm. The maximum temperatures on sunny days were lower in the tilts of the ploughed and in the humps of the cross-directional ploughed sites compared with the unprepared area. Correspondingly, the night temperatures were higher and so the soil preparation considerably reduced the risk of night frost. In the soil at the depth of 5 cm, soil preparation increased daytime temperatures and reduced night temperatures compared with unprepared area. The maximum increase in monthly mean temperatures was almost 5 °C, and the daily variation in the surface parts of the tilts and humps increased so that excessively high temperatures for the optimal growth of the root system were measured from time to time. The temperature also rose at the depths of 50 and 100 cm. Soil preparation also increased the cumulative temperature sum. The highest sums accumulated during the summer months were recorded at the depth of 5 cm in the humps of cross-directional ploughed area (1127 dd.) and in the tilts of the ploughed area (1106 dd.), while the corresponding figure in the unprepared soil was 718 dd. At the height of 10 cm the highest temperature sum was 1020 dd. in the hump, the corresponding figure in the unprepared area being 925 dd. The incidence of high temperature amplitudes and percentage of high temperatures at the depth of 5 cm decreased most rapidly in the humps of cross-directional ploughed area and in the ploughing tilts towards the end of the measurement period. The decrease was attributed principally to the compressing of tilts, the ground vegetation succession and the growth of seedlings. The mean summer temperature in the unprepared area was lower than in the prepared area and the difference did not diminish during the period studied. The increase in temperature brought about by soil preparation thus lasts at least more than 10 years.

Decomposition of Scots pine fine woody debris in boreal conditions

"Litter quality and environmental effects on Scots pine (Pinus sylvestris L.) fine woody debris (FWD) decomposition were examined in three forestry-drained peatlands representing different site types along a climatic gradient from the north boreal (Northern Finland) to south (Southern Finland) and hemiboreal (Central Estonia) conditions. Decomposition (percent mass loss) of FWD with diameter <= 10 mm (twigs) and FWD with diameter > 10 mm (branches) was measured using the litter bag method over 1-4-year periods. Overall, decomposition rates increased from north to south, the rate constants (k values) varying from 0.128 to 0.188 year(-1) and from 0.066 to 0.127 year(-1) for twigs and branches, respectively. On average, twigs had lost 34%, 19% and 19%, and branches 25%, 17% and 11% of their initial mass after 2 years of decomposition at the hemiboreal, south boreal and north boreal sites, respectively. After 4 years at the south boreal site the values were 48% for twigs and 42% for branches. Based on earlier studies, we suggest that the decomposition rates that we determined may be used for estimating Scots pine FWD decomposition in the boreal zone, also in upland forests. Explanatory models accounted for 50.4% and 71.2% of the total variation in FWD decomposition rates when the first two and all years were considered, respectively. The variables most related to FWD decomposition included the initial ash, water extractives and Klason lignin content of litter, and cumulative site precipitation minus potential evapotranspiration. Simulations of inputs and decomposition of Scots pine FWD and needle litter in south boreal conditions over a 60-year period showed that 72 g m(-2) of organic matter from FWD vs. 365 g m(-2) from needles accumulated in the forest floor. The annual inputs varied from 5.7 to 15.6 g m(-2) and from 92 to 152 g m(-2) for FWD and needles, respectively. Each thinning caused an increase in FWD inputs, Up to 510 g m(-2), while the needle inputs did not change dramatically. Because the annual FWD inputs were lowered following the thinnings, the overall effect of thinnings on C accumulation from FWD was slightly negative. The contribution of FWD to soil C accumulation, relative to needle litter, seems to be rather minor in boreal Scots pine forests. (C) 2008 Elsevier B.V. All rights reserved."