Type II aromatic polyketide biosynthetic tailoring enzymes: diversity and adaptation in Streptomyces secondary metabolism.

Members of the bacterial genus Streptomyces are well known for their ability to produce an exceptionally wide selection of diverse secondary metabolites. These include natural bioactive chemical compounds which have potential applications in medicine, agriculture and other fields of commerce. The outstanding biosynthetic capacity derives from the characteristic genetic flexibility of Streptomyces secondary metabolism pathways: i) Clustering of the biosynthetic genes in chromosome regions redundant for vital primary functions, and ii) the presence of numerous genetic elements within these regions which facilitate DNA rearrangement and transfer between non-progeny species. Decades of intensive genetic research on the organization and function of the biosynthetic routes has led to a variety of molecular biology applications, which can be used to expand the diversity of compounds synthesized. These include techniques which, for example, allow modification and artificial construction of novel pathways, and enable gene-level detection of silent secondary metabolite clusters. Over the years the research has expanded to cover molecular-level analysis of the enzymes responsible for the individual catalytic reactions. In vitro studies of the enzymes provide a detailed insight into their catalytic functions, mechanisms, substrate specificities, interactions and stereochemical determinants. These are factors that are essential for the thorough understanding and rational design of novel biosynthetic routes. The current study is a part of a more extensive research project (Antibiotic Biosynthetic Enzymes; www.sci.utu.fi/projects/biokemia/abe), which focuses on the post-PKS tailoring enzymes involved in various type II aromatic polyketide biosynthetic pathways in Streptomyces bacteria. The initiative here was to investigate specific catalytic steps in anthracycline and angucycline biosynthesis through in vitro biochemical enzyme characterization and structural enzymology. The objectives were to elucidate detailed mechanisms and enzyme-level interactions which cannot be resolved by in vivo genetic studies alone. The first part of the experimental work concerns the homologous polyketide cyclases SnoaL and AknH. These catalyze the closure of the last carbon ring of the tetracyclic carbon frame common to all anthracycline-type compounds. The second part of the study primarily deals with tailoring enzymes PgaE (and its homolog CabE) and PgaM, which are responsible for a cascade of sequential modification reactions in angucycline biosynthesis. The results complemented earlier in vivo findings and confirmed the enzyme functions in vitro. Importantly, we were able to identify the amino acid -level determinants that influence AknH and SnoaL stereoselectivity and to determine the complex biosynthetic steps of the angucycline oxygenation cascade of PgaE and PgaM. In addition, the findings revealed interesting cases of enzyme-level adaptation, as some of the catalytic mechanisms did not coincide with those described for characterised homologs or enzymes of known function. Specifically, SnoaL and AknH were shown to employ a novel acid-base mechanism for aldol condenzation, whereas the hydroxylation reaction catalysed by PgaM involved unexpected oxygen chemistry. Owing to a gene-level fusion of two ancestral reading frames, PgaM was also shown to adopt an unusual quaternary sturucture, a non-covalent fusion complex of two alternative forms of the protein. Furthermore, the work highlighted some common themes encountered in polyketide biosynthetic pathways such as enzyme substrate specificity and intermediate reactivity. These are discussed in the final chapters of the work.

Statistical Optimum Design of Heat Exchangers

The optimal design of a heat exchanger system is based on given model parameters together with given standard ranges for machine design variables. The goals set for minimizing the Life Cycle Cost (LCC) function which represents the price of the saved energy, for maximizing the momentary heat recovery output with given constraints satisfied and taking into account the uncertainty in the models were successfully done. Nondominated Sorting Genetic Algorithm II (NSGA-II) for the design optimization of a system is presented and implemented inMatlab environment. Markov ChainMonte Carlo (MCMC) methods are also used to take into account the uncertainty in themodels. Results show that the price of saved energy can be optimized. A wet heat exchanger is found to be more efficient and beneficial than a dry heat exchanger even though its construction is expensive (160 EUR/m2) compared to the construction of a dry heat exchanger (50 EUR/m2). It has been found that the longer lifetime weights higher CAPEX and lower OPEX and vice versa, and the effect of the uncertainty in the models has been identified in a simplified case of minimizing the area of a dry heat exchanger.

Heat Transfer in Plate Heat Exchangers

This study illustrates the different types of plate heat exchangers that are commonly used in various domestic and industrial applications. The main purpose of this paper was to devise a methodology that is capable of calculating optimum number of plates in the design of a plate heat exchanger. To obtain the appropriate number of plates, typically several iterations must be made before a final acceptable design is completed, since plate amount depends on many factors such as, flow velocities, physical properties of the streams, flow channel geometry, allowable pressure drop, plate dimensions, and the gap between the plates. The methodology presented here can be used as a general guide for designing a plate heat exchanger. To investigate the effects of relevant parameters on the thermal-hydraulic design of a plate heat exchanger, several experiments were carried out for single-phase and counter flow arrangement with two brazed plate heat exchangers by varying the flow rates and the inlet temperatures of the fluid streams. The actual heat transfer coefficients obtained based on the experiment were nearly close to the calculated values and to improve the design, a correction factor was introduced. Besides, the effect of flow channel velocity on the pressure drop inside the unit is presented.

Heat transfer in superheaters of the bubbling fluidized bed boiler conversions

It is often reasonable to convert old boiler to bubbling fluidized bed boiler instead of building a new one. Converted boiler consists of old and new heat surfaces which must be fitted to operate together. Prediction of heat transfer in not so ideal conditions sets challenges for designers. Two converted boilers situated in Poland were studied on the grounds of acceptance tests and further studies. Calculation of boiler process was performed with boiler design program. Main interest was heat transfer in superheaters and factors affecting it. Theory for heat transfer is presented according to information found from literature. Results obtained from experimental studies and calculations have been compared. With correct definitions calculated parameters corresponded well to measured data at boiler maximum design load. However overload situations revealed to be difficult to model at least without considering changes in the combustion process which requires readjustments to the design program input values.

A three dimensional study of heat transfer in a supercritical circulating fluidized bed combustor

From the boiler design point of view, it is imperative to know and understand the operation of the boiler. Since comprehensive measurement of a large furnace is impossible, the furnace can be modeled in order to study its behavior and phenomena. This requires the used model to be validated to correspond with the physical furnace behavior. In this thesis, a three dimensional furnace model is validated to match a bituminous coal utilizing, supercritical once-through circulating fluidized bed combustor based on measurement data. The validated model is used for analyzing the furnace heat transfer. Other heat transfer analysis methods are energy balance method based on tube surface temperature measurements and a method based on measured temperature difference between the tube crest and the fin. The latter method was developed in the thesis using Fluent-software. In the theory part, literature is reviewed and the fundamental aspects of circulating fluidized bed are discussed. These aspects are solid particle behavior in fluidization known as hydrodynamics, behavior of fuel and combustion and heat transfer. Fundamental aspects of modeling are also presented.

Statistical Analysis and Numerics of Heat Exchanger Models

The identifiability of the parameters of a heat exchanger model without phase change was studied in this Master’s thesis using synthetically made data. A fast, two-step Markov chain Monte Carlo method (MCMC) was tested with a couple of case studies and a heat exchanger model. The two-step MCMC-method worked well and decreased the computation time compared to the traditional MCMC-method. The effect of measurement accuracy of certain control variables to the identifiability of parameters was also studied. The accuracy used did not seem to have a remarkable effect to the identifiability of parameters. The use of the posterior distribution of parameters in different heat exchanger geometries was studied. It would be computationally most efficient to use the same posterior distribution among different geometries in the optimisation of heat exchanger networks. According to the results, this was possible in the case when the frontal surface areas were the same among different geometries. In the other cases the same posterior distribution can be used for optimisation too, but that will give a wider predictive distribution as a result. For condensing surface heat exchangers the numerical stability of the simulation model was studied. As a result, a stable algorithm was developed.

Lipase-catalyzed Approaches towards Secondary Alcohols: Intermediates for Enantiopure Drugs

The use of enantiopure intermediates for drug synthesis is a trend in pharmaceutical industry. Different physiological effects are associated with the enantiomers of chiral molecules. Thus, the safety profile of a drug based on an enantiopure active pharmaceutical ingredient is more reliable. Biocatalysis is an important tool to access enantiopure molecules. In biocatalysis, the advantage of selectivity (chemo-, regio- and stereoselectivity) is combined with the benefits of a green synthesis strategy. Chemoenzymatic syntheses of drug molecules, obtained by combining biocatalysis with modern chemical synthesis steps usually consists of fewer reaction steps, reduced waste production and improved overall synthetic efficiency both in yields and enantio- and/or diastereoselectivities compared with classical chemical synthesis. The experimental work together with the literature review clearly indicates that lipase catalysis is highly applicable in the synthesis of enantiopure intermediates of drug molecules as the basis to infer the correct stereochemistry. By lipase catalysis, enantiopure secondary alcohols used as intermediates in the synthesis of Dorzolamide, an antiglaucoma drug, were obtained. Enantiopure _-hydroxy nitriles as potential intermediates for the synthesis of antidepressant drugs with 1-aryl-3- methylaminopropan-1-ol structure were also obtained with lipases. Kinetic resolution of racemates was the main biocatalytic approach applied. Candida Antarctica lipase B, Burkholderia cepacia lipase and Thermomyces lanuginosus lipase were applied for the acylation of alcohols and the alcoholysis of their esters in organic solvents, such as in diisopropyl ether and tert-butyl methyl ether. Candida Antarctica lipase B was used under solvent free conditions for the acylation of ethyl 3-hydroxybutanoate.

Methods for construction and analysis of computational models in systems biology : applications to the modelling of the heat shock response and the self-assembly of intermediate filaments

Systems biology is a new, emerging and rapidly developing, multidisciplinary research field that aims to study biochemical and biological systems from a holistic perspective, with the goal of providing a comprehensive, system- level understanding of cellular behaviour. In this way, it addresses one of the greatest challenges faced by contemporary biology, which is to compre- hend the function of complex biological systems. Systems biology combines various methods that originate from scientific disciplines such as molecu- lar biology, chemistry, engineering sciences, mathematics, computer science and systems theory. Systems biology, unlike “traditional” biology, focuses on high-level concepts such as: network, component, robustness, efficiency, control, regulation, hierarchical design, synchronization, concurrency, and many others. The very terminology of systems biology is “foreign” to “tra- ditional” biology, marks its drastic shift in the research paradigm and it indicates close linkage of systems biology to computer science. One of the basic tools utilized in systems biology is the mathematical modelling of life processes tightly linked to experimental practice. The stud- ies contained in this thesis revolve around a number of challenges commonly encountered in the computational modelling in systems biology. The re- search comprises of the development and application of a broad range of methods originating in the fields of computer science and mathematics for construction and analysis of computational models in systems biology. In particular, the performed research is setup in the context of two biolog- ical phenomena chosen as modelling case studies: 1) the eukaryotic heat shock response and 2) the in vitro self-assembly of intermediate filaments, one of the main constituents of the cytoskeleton. The range of presented approaches spans from heuristic, through numerical and statistical to ana- lytical methods applied in the effort to formally describe and analyse the two biological processes. We notice however, that although applied to cer- tain case studies, the presented methods are not limited to them and can be utilized in the analysis of other biological mechanisms as well as com- plex systems in general. The full range of developed and applied modelling techniques as well as model analysis methodologies constitutes a rich mod- elling framework. Moreover, the presentation of the developed methods, their application to the two case studies and the discussions concerning their potentials and limitations point to the difficulties and challenges one encounters in computational modelling of biological systems. The problems of model identifiability, model comparison, model refinement, model inte- gration and extension, choice of the proper modelling framework and level of abstraction, or the choice of the proper scope of the model run through this thesis.

Role and regulatory mechanisms of heat shock factor 2

Protein homeostasis is essential for cells to prosper and survive. Various forms of stress, such as elevated temperatures, oxidative stress, heavy metals or bacterial infections cause protein damage, which might lead to improper folding and formation of toxic protein aggregates. Protein aggregation is associated with serious pathological conditions such as Alzheimer’s and Huntington’s disease. The heat shock response is a defense mechanism that protects the cell against protein-damaging stress. Its ancient origin and high conservation among eukaryotes suggest that the response is crucial for survival. The main regulator of the heat shock response is the transcription factor heat shock factor 1 (HSF1), which induces transcription of genes encoding protective molecular chaperones. In vertebrates, a family of four HSFs exists (HSF1-4), with versatile functions not only in coping with acute stress, but also in development, longevity and cancer. Thus, knowledge of the HSFs will aid in our understanding on how cells survive suboptimal circumstances, but will also provide insights into normal physiological processes as well as diseaseassociated conditions. In this study, the function and regulation of HSF2 have been investigated. Earlier gene inactivation experiments in mice have revealed roles for HSF2 in development, particularly in corticogenesis and spermatogenesis. Here, we demonstrate that HSF2 holds a role also in the heat shock response and influences stress-induced expression of heat shock proteins. Intriguingly, DNA-binding activity of HSF2 upon stress was dependent on the presence of intact HSF1, suggesting functional interplay between HSF1 and HSF2. The underlying mechanism for this phenomenon could be configuration of heterotrimers between the two factors, a possibility that was experimentally verified. By changing the levels of HSF2, the expression of HSF1-HSF2 heterotrimer target genes was altered, implementing HSF2 as a modulator of HSF-mediated transcription. The results further indicate that HSF2 activity is dependent on its concentration, which led us to ask the question of how accurate HSF2 levels are achieved. Using mouse spermatogenesis as a model system, HSF2 was found to be under direct control of miR-18, a miRNA belonging to the miR-17~92 cluster/Oncomir-1 and whose physiological function had remained unclear. Investigations on spermatogenesis are severely hampered by the lack of cell systems that would mimic the complex differentiation processes that constitute male germ cell development. Therefore, to verify that HSF2 is regulated by miR-18 in spermatogenesis, a novel method named T-GIST (Transfection of Germ cells in Intact Seminiferous Tubules) was developed. Employing this method, the functional consequences of miR-18-mediated regulation in vivo were demonstrated; inhibition of miR- 18 led to increased expression of HSF2 and altered the expression of HSF2 target genes Ssty2 and Speer4a. Consequently, the results link miR-18 to HSF2-mediated processes such as germ cell maturation and quality control and provide miR-18 with a physiological role in gene expression during spermatogenesis.Taken together, this study presents compelling evidence that HSF2 is a transcriptional regulator in the heat shock response and establishes the concept of physical interplay between HSF2 and HSF1 and functional consequences thereof. This is also the first study describing miRNA-mediated regulation of an HSF.

Middle school mediocrity : quality and inequality in secondary education

Centrala teman i min avhandling är parallellskolesystem, linjedelning och segregering i högstadier och gymnasier. Det finns stora skillnader mellan länder gällande den årskurs då eleverna sorteras in i olika nivåer genom skilda klasser eller skolor. I Tyskland och Nederländerna till exempel delas eleverna upp före högstadiet medan Sverige och Finland har enhetsskolor på högstadienivå. Jag argumenterar att parallellskolesystem har en positiv effekt på elevernas testresultat i årskurserna före linjedelningen. Eleverna har incitament att jobba hårdare för att komma på i den akademiska linjen. Jag undersöker incitamentseffekter empiriskt, och hittar mönster konsistenta med incitamentseffekter både i brittisk och i internationell data. Det andra bidraget i avhandlingen är metodologiskt. Nationalekonomer brukar behandla testresultat från t.ex. IQ-tester eller internationella PISA-undersökningar som om absoluta nivån på poängantalen har betydelse i sig. I verkligheten antyder de endast en rangordning. Jag visar att normalfördelade testresultat i många fall ligger tillräckligt nära dess pengavärde på arbetsmarknaden för att ändå kunna tolkas som absoluta.

Pragmatic competence of Finnish learners of English: Meaning in interaction in secondary and upper secondary schools

Tutkin pro gradu -tutkielmassani englannin kielen oppijoiden pragmaattista kompetenssia. Tarkoitukseni oli selvittää, miten suomalaiset yläkoululaiset ja lukiolaiset osaavat käyttää englannin kieltä erilaisissa kommunikaatiotilanteissa. Tutkielmani voidaan sijoittaa välikielen pragmatiikan tutkimukseen. Halusin selvittää, millä tasolla suomalaisten oppijoiden pragmaattinen kompetenssi on ja kehittyykö se yläkoulun ja lukion välillä. Lisäksi tutkin, vaikuttavatko oppimisympäristö ja oppimismahdollisuudet oppijoiden kykyyn käyttää englannin kieltä. Toisin sanoen vertasin englantipainotteisilla luokilla olevia oppilaita formaalin opetuksen oppijoihin sekä tutkin, vaikuttavatko englanninkieliset vapaa-ajan aktiviteetit ja oppijoiden mahdolliset oleskelut englanninkielisissä maissa heidän pragmaattiseen kompetenssiinsa. Tutkimukseni kohderyhmä koostui yläkoulun kahdeksasluokkalaisista ja lukion toisen vuosikurssin opiskelijoista. Testasin neljä eri ryhmää, joissa oli sekä formaalissa opetuksessa olevia oppijoita (yksi ryhmä kahdeksasluokkalaisia ja yksi ryhmä toisen vuosikurssin opiskelijoita) että kielipainotteisten luokkien oppijoita (yksi ryhmä kahdeksasluokkalaisia ja yksi ryhmä toisen vuosikurssin opiskelijoita). Arvioin kohderyhmäni pragmaattista kompetenssia monivalintatestillä, jossa testattiin oppijoiden kykyä käyttää ja ymmärtää implikaatioita, tilannekohtaisia rutiineja sekä puheakteja. Taustakysymysten avulla selvitin, kuinka usein oppijat käyttivät englantia vapaa-aikanaan ja olivatko he vierailleet englanninkielisissä maissa. Tutkimustulokseni osoittavat, että suomalaisten yläkoululaisten ja lukiolaisten pragmaattinen kompetenssi oli korkea. Pragmaattinen kompetenssi kehittyi kahdeksasluokkalaisten ja lukion toisen vuosikurssin välillä. Kehitys oli suurempaa formaalissa opetuksessa kuin kielipainotteisilla luokilla. Englantipainotteisilla luokilla olevat oppilaat suoriutuivat testistä paremmin kuin formaalin opetuksen oppilaat. Tosin erot olivat tilastollisesti merkitseviä vain yläkoulussa. Tutkimuksessani siis päättelin, että vieraskielinen opetus vaikutti enemmän nuorempiin oppijoihin. Eri oppimismahdollisuudet osoittautuivat haastaviksi analysoida. Tulokset osoittivat, että vain englanninkielisessä maassa oleskelulla oli vaikutusta oppijoiden pragmaattiseen kompetenssiin. Kysyttäessä vapaa-ajan aktiviteettien merkitystä oppijat kuitenkin kertoivat, että ne auttoivat heitä testiin vastaamisessa enemmän kuin englanninopetuksessa käydyt asiat. Kouluissa tulisikin jatkossa painottaa yhä enemmän vuorovaikutteista kieltenopetusta.

Prosessihöyryn tuotannon kustannusoptimointi

Tässä työssä on tutkittu prosessihöyryn tuotantokustannusten optimointia Neste Oil Oy:n Naantalin jalostamolla. Työssä on keskitytty ennen kaikkea prosessi-höyryn tuotantoon öljynjalostamolla. Tavoitteena oli luoda yksinkertainen työkalu, jonka avulla voidaan vertailla höyryntuotantokustannuksia jalostamon tuotan-toyksiköissä. Samalla oli tarkoituksena kartoittaa höyryn tuotantomahdollisuudet yksiköissä. Työn tuloksena tehty Excel-pohjainen laskentataulukko on esitelty tässä työssä. Ohjelman tarkkuutta on mahdollista parantaa prosessikoeajojen avul-la. Jo nykyisellä laskentatarkkuudella ohjelma täyttää kuitenkin asetetut tavoitteet eli antaa mahdollisuuden vertailla helposti ja havainnollisesti tuotantokustannuksia yksiköiden välillä. Oman höyryntuotannon lisäksi Naantalin jalostamo ostaa höyryä viereiseltä Fortumin Naantalin voimalaitokselta. Ostohöyryn hinta on las-kettu työkalussa mukaan vertailuun. Työn perusteella ostohöyry on Naantalin ja-lostamon tapauksessa selkeästi omatuotantoa edullisempi vaihtoehto. Ero kustan-nuksissa syntyy käytettävästä polttoaineesta, joka jalostamon tapauksessa on ja-lostamo- eli polttokaasu. Nykyisen tasoisella raakaöljyn hinnalla tilanne säilynee tällaisena tulevaisuudessakin. Jalostamolta löytyi myös kohteita, joissa energiatehokkuutta on mahdollista kehit-tää nykyisen höyryverkon ulkopuolella. Esimerkkeinä tällaisista kohteista tässä työssä on tarkasteltu toisen jätelämpökattilan rakentamista nykyisen toiminnassa olevan rinnalle, sekä höyryturbiinien asentamista paineenalennuslinjoihin. Näistä hankkeista jätelämpökattila osoittautui erittäin suositeltavaksi investoinniksi.