Statistical Methods for Conservation and Alignment Quality in Proteins

Construction of multiple sequence alignments is a fundamental task in Bioinformatics. Multiple sequence alignments are used as a prerequisite in many Bioinformatics methods, and subsequently the quality of such methods can be critically dependent on the quality of the alignment. However, automatic construction of a multiple sequence alignment for a set of remotely related sequences does not always provide biologically relevant alignments.Therefore, there is a need for an objective approach for evaluating the quality of automatically aligned sequences. The profile hidden Markov model is a powerful approach in comparative genomics. In the profile hidden Markov model, the symbol probabilities are estimated at each conserved alignment position. This can increase the dimension of parameter space and cause an overfitting problem. These two research problems are both related to conservation. We have developed statistical measures for quantifying the conservation of multiple sequence alignments. Two types of methods are considered, those identifying conserved residues in an alignment position, and those calculating positional conservation scores. The positional conservation score was exploited in a statistical prediction model for assessing the quality of multiple sequence alignments. The residue conservation score was used as part of the emission probability estimation method proposed for profile hidden Markov models. The results of the predicted alignment quality score highly correlated with the correct alignment quality scores, indicating that our method is reliable for assessing the quality of any multiple sequence alignment. The comparison of the emission probability estimation method with the maximum likelihood method showed that the number of estimated parameters in the model was dramatically decreased, while the same level of accuracy was maintained. To conclude, we have shown that conservation can be successfully used in the statistical model for alignment quality assessment and in the estimation of emission probabilities in the profile hidden Markov models.

The Methods of Possible Joint Treatment of Manure and Sewage Sludge in the Leningrad Region

The nutrient load to the Gulf of Finland has started to increase as a result of the strong economic recovery in agriculture and livestock farming in the Leningrad region. Also sludge produced from municipal wastewater treatment plant of the Leningrad region causes the great impact on the environment, but still the main options for its treatment is disposal on the sludge beds or Landfills. The aim of this study was to evaluate the implementation of possible joint treatment methods of manure form livestock and poultry enterprises and sewage sludge produced from municipal wastewater treatment plants in the Leningrad region. The study is based on published data. The most attention was put on the anaerobic digestion and incineration methods. The manure and sewage sludge generation for the whole Leningrad region and energy potential produced from their treatment were estimated. The calculations showed that total amount of sewage sludge generation is 1 348 000 t/a calculated on wet matter and manure generation is 3 445 000 t/a calculated on wet matter. The potential heat release from anaerobic digestion process and incineration process is 4 880 000 GJ/a and 5 950 000 GJ/a, respectively. Furthermore, the work gives the overview of the general Russian and Finnish legislation concerning manure and sewage sludge treatment. In the Gatchina district it was chosen the WWTP and livestock and poultry enterprises for evaluation of the centralized treatment plant implementation based on anaerobic digestion and incineration methods. The electricity and heat power of plant based on biogas combustion process is 4.3 MW and 7.8 MW, respectively. The electricity and heat power of plant based on manure and sewage sludge incineration process is 3.0 MW and 6.1 MW, respectively.

Feasibility of ASH DEC‐ process in treating sewage sludge and manure ash in Finland

In Finland the thermal treatment of sewage sludge has been moderate in 21th century. The reason has been the high moisture content of sludge. During 2005-2008, 97-99% of sewage sludge was utilized in landscaping and agriculture. However agricultural use has been during 2005-2007 less than 3 %. The aim of national waste management plan is that by 2016 100% of sludge is used either as soil amendment or energy. The most popular utilization method for manure is spreading it on arable land. The dry manures such as poultry manure and horse manure could also be used in incineration. The ashes could be used as fertilizers and while it is not suitable as a starter fertilizer, it is suitable in maintaining P levels in the soil. One of the main drivers for more efficient nutrient management is the eutrophication in lakes and the Baltic See. ASH DEC process can be used in concentrating phosphorus rich ashes while separating the heavy metals that could be included. ASH DEC process uses thermochemical treatment to produce renewable phosphate for fertilizer production. The process includes mixing of ashes and chlorine donors and subsequent treatment in rotary kiln for 20 min in temperature of 900 – 1 050 oC. The heavy metals evaporate and P-rich product is obtained. The toxic substances are retained in air pollution control system in form of mixed metal hydroxides. The aim of conducting this study is to estimate the potential of ASH DEC process in treating phosphorus rich ashes in Finland. The masses considered in are sewage sludge, dry manure from horses, and poultry and liquid pig manure. To date the usual treatment method for sewage sludge in Finland is composting or anaerobic digestion. Part of the amount of produced sewage sludge (800 kt/a fresh mass and 160 kt/a TS) could also be incinerated and the residual ashes used in ASH DEC process. Incinerating only manure can be economically difficult to manage because the incineration of manure is in Finland considered as waste incineration. Getting a permit for waste incineration is difficult and also small scale waste incineration is too expensive. The manure could act as an additional feedstock in counties with high density of animal husbandry where the land area might not be enough for spreading of manure. Now when the manure acts as a supplementary feedstock beside sludge, the ash can’t be used directly as fertilizer. Then it could be used in ASH DEC process. The perquisite is that the manure producers could pay for the incineration, which might prove problematic.

Targeted measures bring the greatest benefits for environmental protection in agriculture final report of the TEHO Plus project (2011–2014)

Targeted measures bring the greatest benefits for environmental protection in agriculture final report of the TEHO Plus project (2011–2014). Particular priority areas of the project activities included creating a training package for agri-environment advisers and testing it, farm-specific advisory services and exploitation of experiences of advice provision, putting together an information package of agri-environment issues, farm-level experiments, and development of water quality monitoring. The recommendations issued by advisers on targeting environmental measures were based on utilising geographical information material and nutrient balances. The project was implemented in cooperation by Southwest Finland Centre for Economic Development, Transport and the Environment, MTK-Satakunta and MTK-Varsinais-Suomi. The project received funding from the Ministry of Agriculture and Forestry and the Ministry of the Environment. Participating farmers, with whom environmental advice was developed and experiments were carried out, were important partners for the project. The operating area of the project was Satakunta and Varsinais-Suomi in Southwest Finland, but its outcomes can be exploited nationally. A national perspective was ensured by close cooperation with actors in different provinces. This final report describes project experiences and outcomes including environmental advisory services, training of agri-environmental advisers, farm visits and the feedback received from farmers on agri-environmental advice, development of water quality monitoring, experiments and project work.

JNK regulates dendrite and spine architecture in the central nervous system influencing spatial learning and motor tasks

JNK1 is a MAP-kinase that has proven a significant player in the central nervous system. It regulates brain development and the maintenance of dendrites and axons. Several novel phosphorylation targets of JNK1 were identified in a screen performed in the Coffey lab. These proteins were mainly involved in the regulation of neuronal cytoskeleton, influencing the dynamics and stability of microtubules and actin. These structural proteins form the dynamic backbone for the elaborate architecture of the dendritic tree of a neuron. The initiation and branching of the dendrites requires a dynamic interplay between the cytoskeletal building blocks. Both microtubules and actin are decorated by associated proteins which regulate their dynamics. The dendrite-specific, high molecular weight microtubule associated protein 2 (MAP2) is an abundant protein in the brain, the binding of which stabilizes microtubules and influences their bundling. Its expression in non-neuronal cells induces the formation of neurite-like processes from the cell body, and its function is highly regulated by phosphorylation. JNK1 was shown to phosphorylate the proline-rich domain of MAP2 in vivo in a previous study performed in the group. Here we verify three threonine residues (T1619, T1622 and T1625) as JNK1 targets, the phosphorylation of which increases the binding of MAP2 to microtubules. This binding stabilizes the microtubules and increases process formation in non-neuronal cells. Phosphorylation-site mutants were engineered in the lab. The non-phosphorylatable mutant of MAP2 (MAP2- T1619A, T1622A, T1625A) in these residues fails to bind microtubules, while the pseudo-phosphorylated form, MAP2- T1619D, T1622D, Thr1625D, efficiently binds and induces process formation even without the presence of active JNK1. Ectopic expression of the MAP2- T1619D, T1622D, Thr1625D in vivo in mouse brain led to a striking increase in the branching of cortical layer 2/3 (L2/3) pyramidal neurons, compared to MAP2-WT. The dendritic complexity defines the receptive field of a neuron and dictates the output to the postsynaptic cells. Previous studies in the group indicated altered dendrite architecture of the pyramidal neurons in the Jnk1-/- mouse motor cortex. Here, we used Lucifer Yellow loading and Sholl analysis of neurons in order to study the dendritic branching in more detail. We report a striking, opposing effect in the absence of Jnk1 in the cortical layers 2/3 and 5 of the primary motor cortex. The basal dendrites of pyramidal neurons close to the pial surface at L2/3 show a reduced complexity. In contrast, the L5 neurons, which receive massive input from the L2/3 neurons, show greatly increased branching. Another novel substrate identified for JNK1 was MARCKSL1, a protein that regulates actin dynamics. It is highly expressed in neurons, but also in various cancer tissues. Three phosphorylation target residues for JNK1 were identified, and it was demonstrated that their phosphorylation reduces actin turnover and retards migration of these cells. Actin is the main cytoskeletal component in dendritic spines, the site of most excitatory synapses in pyramidal neurons. The density and gross morphology of the Lucifer Yellow filled dendrites were characterized and we show reduced density and altered morphology of spines in the motor cortex and in the hippocampal area CA3. The dynamic dendritic spines are widely considered to function as the cellular correlate during learning. We used a Morris water maze to test spatial memory. Here, the wild-type mice outperformed the knock-out mice during the acquisition phase of the experiment indicating impaired special memory. The L5 pyramidal neurons of the motor cortex project to the spinal cord and regulate the movement of distinct muscle groups. Thus the altered dendrite morphology in the motor cortex was expected to have an effect on the input-output balance in the signaling from the cortex to the lower motor circuits. A battery of behavioral tests were conducted for the wild-type and Jnk1-/- mice, and the knock-outs performed poorly compared to wild-type mice in tests assessing balance and fine motor movements. This study expands our knowledge of JNK1 as an important regulator of the dendritic fields of neurons and their manifestations in behavior.

Utilization of coal combustion residues in glass manufacturing process

The focus of paper is to asses and evaluate new utilisation method of coals combustion resides in glass manufacturing process. Mathematical model of glass manufacturing material balance was used to find favourable proportion of normally used batch materials and coal ash. It was found that possible to substitute up to 20 % of batch with coal ash. On the world glass production scale there is a potential to save 8,4 million tons of silica sand, 6 million tons of dolomite, 3 million tons of clay and 0,2 million tons of lime borate. Furthermore, potential to utilize 2 % of coal combustion products with suggested method.