Browsing by Title
Now showing items 18813-18832 of 31123
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(2011)The objective of this thesis is to examine the economic effects in the conflict between grey seal population and the salmon fishery in the Baltic Sea. We will formulate a bioeconomic model which provides new insights on the optimal management of Atlantic salmon with respect to the effects brought about by the grey seal population. As the catch losses caused by seals have an effect on salmon fishery in Baltic, we will study how seal population affects the present value of the salmon fishery. The study considers the Finnish coastal trap net fishery. The bioeconomic model considers a scenario of sole salmon fishery and a scenario of salmon fishery affected by the grey seal population. On the basis of these scenarios, a seal compensation scheme is introduced. We can observe a significant economic seal-induced effect on the salmon fishery. The results suggest that the present seal compensation scheme emploid by the Finnish government is suboptimal. This thesis is part of the TARMO –project, in which the conflict between grey seal population and salmon fishery is studied using the methods of environmental economics.
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(2013)The purpose of this study was to define economically optimal stand structures and harvesting cycles for uneven-aged Scots pine (Pinus sylvestris L.) in Finland. According to a recent proposal by Ministry of Agriculture and Forestry, uneven-aged management will be included in the new Forest Act as an alternative for future forest management in Finland. Uneven-aged management is also planned to be included in the Forest management practice recommendations by the year 2014. However, only little knowledge exists on optimal uneven-aged management in Finland, particularly on uneven-aged Scots pine. This thesis aimed at filling the gap in knowledge regarding economically optimal management of uneven-aged Scots pine. So far, economic studies on uneven-aged Scots pine have been conducted only in a static optimization framework, where optimal stand structure is constrained with a classic “reversed-J” diameter distribution, and transition cuttings are limited to one single harvest. In this work, stand structures and harvesting cycles were optimized for maximum volume yield and maximum stumpage revenues by applying both static and dynamic optimization. Until now, no dynamic optimization has been conducted on uneven-aged Scots pine. Static optimization was applied for different growth sites from mesic sites in Southern Finland (MT1300) to sub-xeric sites in Central Finland (VT1100). Mesic sites in Southern Finland were also optimized in a dynamic framework. A density-dependent individual tree model with latest ecological growth models was applied in optimization. The large-scale nonlinear problems were solved by means of numerical computing with discrete-time formulations. Present value of stumpage revenues was maximized applying 1% and 3% discount rates. Economically optimal harvesting cycle became 40 years in Southern Finland (site MT1300), and even longer at more northern and less fertile site types. Results imply that it is not economically optimal to manage Scots pine with a traditional selection method with short harvesting cycles, but rather with a heavy harvesting regime including low after cut basal areas. When maximizing present value of stumpage revenues, optimal after cut basal areas in Southern Finland were as low as 5 m2 (1% discount rate) and 3.2 m2 (3% discount rate) per hectare. A proposal of Ministry of Agriculture and Forestry suggests minimum after cut basal areas of 10–11 m2 per hectare for Southern Finland, which clearly exceed the optima of this study. Contrary to the existing results for uneven-aged Scots pine, economically optimal stand structure did not follow the classic reversed-J diameter distribution.
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(2011)The aim of the thesis is to assess the fishery of Baltic cod, herring and sprat by simulation over 50 years time period. We form a bioeconomic multispecies model for the species. We include species interactions into the model because especially cod and sprat stocks have significant effects on each other. We model the development of population dynamics, catches and profits of the fishery with current fishing mortalities, as well as with the optimal profit maximizing fishing mortalities. Thus, we see how the fishery would develop with current mortalities, and how the fishery should be developed in order to yield maximal profits. Especially cod stock has been quite low recently and by optimizing the fishing mortality it could get recovered. In addition, we assess what would happen to the fisheries of the species if more favourable environmental conditions for cod recruitment dominate in the Baltic Sea. The results may yield new information for the fisheries management. According to the results the fishery of Baltic cod, herring and sprat are not at the most profitable level. The fishing mortalities of each species should be lower in order to maximize the profits. By fishing mortality optimizing the net present value would be almost three times higher in the simulation period. The lower fishing mortality of cod would result in a cod stock recovery. If the environmental conditions in the Baltic Sea improved, cod stock would recover even without a decrease in the fishing mortality. Then the increased cod stock would restrict herring and sprat stock remarkably, and harvesting of these species would not be as profitable anymore.
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(2021)Aquaculture is seen as an answer to the future’s projected demand increase of seafood. This offers possibilities for the Finnish society to benefit economically. Globally, environmental concerns are set to the pressure the future demand, since the sector’s production is jointly linked to creating negative outputs, nutrient emissions. These problems are especially present in Finland, which’s offshore aquaculture production occurs geographically in one of the world’s most eutrophicated seas, the Baltic Sea. Finnish aquaculture regulation is currently a type of “command and control”, which is seen as one of the main reasons why the domestic production has decreased drastically in 21st century. Continuing to utilize feed quotas may not sufficient and incentivizing for the producers which creates need to review other possible economic instruments. This research studies the possibility of utilizing auctioned emission permits. The work contributes to auction theory of incomplete information games while adding Baltic Sea elements such as abatement costs to our analyzed model. This thesis addresses three questions: How can the chosen auction models support sustainable growth of aquaculture in economically efficient way? What is the level of optimal price floor? Which auction form is expected to create highest revenue surplus for the society? The policy maker is interested in assessing which of the chosen auction models is best allocation tool under present asymmetrical information. To combat the missing information on production values per kilogram of nitrate, Monte Carlo-simulation is utilized to generate values for the bidding producers. The analysis creates premise of including price floor in the mechanism designs to guarantee sustainability. The price floor guarantees that the value of allocated permit will be at least the size of our adopted abatement costs, which originate from certain mussel cultivation farm located in Sankt Anna, Sweden. The effects of two potential price floors are analyzed. First, which secures sustainability and second, which maximizes expected revenue surplus. Our modelled results follow the findings of the theory. All chosen auction designs are expected to create similar results in allocating the emission permits. To secure that the allocated permits are sustainable, and that the allocation maximize society’s revenue surplus, the social planner should implement price floor which is strictly higher than his personal valuation of the permit. This removes the possibility of auction being ex-ante efficient. Even though in the chosen model setting the price floor’s level was not dependent on the level of buyers, the social planner should not ignore the aspect of competition. By designing a mechanism that enables easy entry for bidders to participate, the auctions are expected to attract higher levels of competition which can create results that are closer to competitive markets. This can decrease the role of price floor, which may ease mechanism designing. To get more accurate results in the Finnish scene, more detailed information on possible domestic aquaculture production values is needed
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(2016)Quantum computers store and manipulate information in individual quantized energy levels. These devices, not yet realized in their full potential, have the ability to perform certain computational tasks more efficiently than any classical computer. One possible way to implement a quantum computer is to use superconducting circuits controlled by single-mode electromagnetic fields. These circuits constitute the physical quantum bits, or qubits, that are used to store quantum information. A complete, fault-tolerant quantum computer potentially consists of at least millions of physical qubits which are grouped to form fault-tolerant logical qubits. Controlling each physical qubit individually requires a great amount of energy, and hence a future challenge is to reduce the energy consumption in qubit control while maintaining the high precision. In this thesis, we derive a fundamental upper bound for the gate fidelity of a single-qubit not gate implemented with a single resonant driving pulse. It is shown that the upper bound approaches unity inversely proportionally to the increasing mean photon number of the pulse. Furthermore, we find that the upper bound is achieved with an optimal superposition of squeezed states. The typically employed coherent state produces twice as high gate error as the corresponding optimal state. In addition, we present and numerically study a correction protocol that allows using the same drive state for multiple qubit operations. This sustained state is refreshed by sequentially coupling ancillary qubits to it, effectively resetting it and removing entanglement with the previously operated qubits. Thus our protocol allows using the same drive state to implement not gates for different qubits indefinitely, and hence provides a possible route to energy-efficient large-scale quantum computing.
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(2013)In this thesis we study the notion of non-negative Ricci curvature for compact metric measure spaces introduced by Lott and Villani in their article (2009): Ricci curvature for metric measure spaces via optimal transport. We also define and prove the required prerequisites concerning length spaces, convex analysis, measure theory, and optimal transportation.
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(2017)Numeriska väderprognosmodeller (NWP, numerical weather prediction) innehåller variabler, såsom vindvektorer, temperatur och tryck, samt modellparametrar. Modellparametrar är en oundviklig del av en NWP då de behövs i parametriseringsscheman av småskaliga fysikaliska processer. Modellparametrarna har betydelse för modellens förmåga att prognostisera vädret och det är därav av stor vikt att parametrarna har optimala värden. Värdet på parametrarna bestäms manuellt med hjälp av observationer och expertkunskap, vilket är en arbetsdryg process. För att minska på arbetsbördan och frigöra resurser för annat är det möjligt att använda sig av algoritmer för att bestämma de optimala värdena på modellparametrarna. I den här studien undersöker vi en statistisk algoritm som används i ett ensembleprognossystem. Algoritmen grundar sig på att uppdatera och förbättra parametervärdena baserat på observationer och en kostnadsfunktion. Tidigare resultat har visat att algoritmen ger goda resultat med en ensemble på 50 medlemmar. I den här studien undersöks huruvida det är möjligt att minska ensemblestorleken vid optimering av två parametrar och samtidigt uppnå goda resultat. I experimenten används Lorenz96-modellen för att emulera NWP och ensemblestorleken varieras mellan två och 50. Resultaten tyder på att en ensemblestorlek på fyra ger goda resultat då utgångsläget är optimalt och vid mindre optimala förhållanden krävs flera ensemblemedlemmar; i det här fallet tio. Baserat på de här experimenten kan vi dra slutsatsen att algoritmen inte begränsas av ensemblestorleken utan snarare av modellen och utgångsläget vid parameteroptimering. Ju bättre utgångsläget är, desto mindre ensemble är möjlig att använda. Experimenten indikerar på att motsvarande resultat är att vänta för NWP.
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(2023)Filamentous fungus Trichoderma reesei (teleomorph Hypocrea jecorina) is a crucial production organism for enzymes used in industrial applications, such as in feed, food, textile, and biofuel production, due to its ability to secrete high amounts of homologous and heterologous enzymes. Therefore, development of genetic tools to improve the properties of industrial T. reesei strains for even better production yields is essential. In this study, a polyethylene glycol mediated CRISPR-Cas9 transformation method for industrial T. reesei production strains was aimed to be optimised by testing an alternative Cas9 enzyme and varying the stoichiometry and total amount of Cas9 enzyme and single guide RNA in the ribonucleoprotein complex. Correct integration of the gene constructions in the obtained transformants was determined by colony PCR and Southern blot analysis. In addition, two selected background activity encoding genes, endoglucanase 6 and α-glucuronidase 1, were individually deleted from T. reesei xylanase production strain utilising the improved CRISPR-Cas9 transformation protocol. The effect of background activity deletions on the strain growth and protein production were analysed from culture supernatants by pH measurement, Bradford protein assay, sodium dodecyl sulfate polyacrylamide gel electrophoresis, and enzyme activity assays. An improved CRISPR-Cas9 transformation protocol for T. reesei was successfully established basing on high number of transformants and improved DNA integration fidelity. No negative effects were observed in the growth or protein production properties of the background activity deletion strains compared to the xylanase production strain. Thus, further cleansing of T. reesei secretome can be continued to refine the industrial production strains.
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(2023)The aim of this work is to develop and optimise an atmospheric inverse modelling system to estimate local methane (CH4) emissions in peatlands. Peatlands are a major source of CH4 regionally in boreal areas and they have significance on a global scale as a soil carbon storage. Data assimilation in the inverse modelling system is based on an ensemble Kalman filter (EnKF) which is widely used in global and regional atmospheric inverse models. The EnKF in this study is an implementation of the EnKF used in the global atmospheric inversion model CarbonTracker Europe-CH4 (CTE-CH4) applied to local setting in the peatland. Consistency of the methodology with regional and global models means that it is possible to expand the system in scale. Siikaneva fen in Southern Finland is used as a testbed for the optimisation of the system. Prior natural CH4 fluxes in Siikaneva are acquired from the HelsinkI Model of MEthane buiLd-up and emIssion for peatland (HIMMELI) which simulates exchange of gases in peatlands. In addition to the peatland fluxes, anthropogenic fluxes at the site are estimated as well in the inversion. For the assimilation of atmospheric CH4 concentration observations, the CH4 fluxes are transformed into atmospheric concentration with a simple one-dimensional box model. The optimisation of the system was done by changing parameters in the model which affect the data assimilation. In model optimisation tests it was discovered that the performance of the modelling system is unstable. There was large variability in the produced estimates between consecutive model runs. Model evaluation statistics did not indicate improvement of the estimates after the inversion. No exact reason for the unstability was able to be determined. Posterior estimates of CH4 fluxes for years 2012–2015 did not differ much from prior estimates and they had large uncertainty. However, evaluation against flux measurements showed reasonable agreement and posterior concentration estimates were within the uncertainty range of the observed concentration.
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(2022)Tutkielma käsittelee optimismivinouman esiintymistä tulevaisuusskenaarioissa, joiden aiheena on ilmastonmuutos. Siinä missä skenaariomenetelmän käyttö voi vähentää tiettyjen kognitiivisten vinoumien vaikutusta tulevaisuutta koskevissa arvioissa, toiset vinoumat voivat puolestaan haitata skenaarioiden laatimista ja arviointia. On arveltu, että useissa eri konteksteissa esiintyvä optimismivinouma näyttäytyisi myös skenaariomenetelmän yhteydessä. Tutkimus selvittää kokeellisesti, esiintyykö ilmastonmuutosaiheisten skenaarioiden arvioinneissa optimismivinoumaa, eli pitävätkö koehenkilöt positiivisia skenaarioita muita todennäköisempinä. Lisäksi tarkastellaan, onko skenaario-optimismi yhteydessä optimismivinoumaan toisessa kontekstissa mitattuna sekä muihin muuttujiin. Tutkimuskysymysten selvittämiseksi koostettiin kyselylomake, joka lähetettiin Helsingin yliopiston ainejärjestöjen sähköpostilistoille. Kyselyyn tuli 182 vastausta. Tutkittaville esitettiin neljä skenaariota, jotka vaihtelivat positiivisesta negatiiviseen, ja ne käsittelivät saimaannorpan selviytymistä ja kannan kokoa 50 vuoden päästä. Koehenkilöiden tuli asettaa skenaariot todennäköisyysjärjestykseen, jonka pohjalta kullekin vastaajalle laskettiin tietty optimistisuuden taso. Keskimäärin vastaajat olivat pessimistisiä arvioissaan, ja tämä optimistisuuslukema jäi alle neutraalina pidetyn arvon. Skenaarioarvioissa ei siis esiintynyt optimismivinoumaa. Optimismivinoumaa mitattiin myös laittamalla koehenkilöt arvioimaan eri elämäntapahtumien todennäköisyyksiä omalla kohdallaan verrattuna muihin. Näissä kysymyksissä optimismivinoumaa esiintyi, sillä vastaajat arvelivat keskimäärin kokevansa positiivisia tapahtumia muita todennäköisemmin ja negatiivisia muita epätodennäköisemmin. Elämäntapahtumaoptimismin määrä myös korreloi positiivisesti skenaario-optimismin kanssa. Lomakkeella selvitettiin myös muiden muuttujien yhteyttä skenaarioarviointien mahdolliseen optimismivinoumaan. Yleisen optimismin tasoa selvitettiin valmiilla kyselyllä, mutta tämä ei korreloinut skenaario-optimismin kanssa. Ilmastonmuutosasenne puolestaan korreloi negatiivisesti skenaario-optimismin kanssa, eli ilmastonmuutokseen vakavasti suhtautuvat arvioivat skenaarioita pessimistisemmin. Vastaajien ikä, sukupuoli tai saimaannorppatiedon määrä ei vaikuttanut skenaarioarviointeihin. Optimismivinouman puute skenaarioarvioissa oli yllättävä tulos, jonka tarkkaa syytä ei voida sanoa täsmällisesti. Tämä voi johtua joko skenaariomenetelmän kognitiivisia vinoumia vähentävästä vaikutuksesta tai skenaarioiden aiheena olleen ilmastonmuutoksen herättämistä negatiivisista mielikuvista. Olisikin tarvetta tutkia aihetta lisää edustavammalla otoksella sekä tutkimusasetelmalla, joka erottelisi skenaariomenetelmän ja ilmastonmuutosaiheen vaikutukset toisistaan. Skenaarioiden käytön kannalta optimismivinouman puute voidaan kuitenkin nähdä hyvänä asiana.
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(2022)Severe acute respiratory syndrome coronavirus 2 is the pathogen behind COVID-19, a contagious disease that has caused millions of deaths since the beginning of the global pandemic in 2019. It is essential to gain more knowledge about the factors affecting viral entry and infection to understand prevention and treatment possibilities for the pathogen. Initially, an immunostaining assay was set up and showed that at eight hours post-infection, the virus had entered the target cells and started protein production. Five host genes of interest, identified by collaborators, were transiently silenced using small interfering RNA knockdown of cell lines. Once the silencing had been optimized, the effect on SARS-CoV-2 infection was monitored at eight and 24 h post-infection. The main pipeline used to follow the cell entry and replication was an extraction of total RNA, reverse transcription reaction followed by quantitative digital droplet polymerase chain reaction, showing the concentrations of the expressed target genes in the cells. The protocols of the transfection and ddPCR were tested and optimized to provide reproducible and reliable results. Out of six tested transfection reagents, DharmaFECT 2 showed the most effective results, decreasing the expression of target genes DDX3X and PDE4A by more than 75% after a 24 h incubation. The produced knockdown cells were infected with a produced and purified stock of SARS-CoV-2. Plaque assays were made from samples collected 24 hours post-infection, but no difference could be seen in the titer of the virus between the transfected cells and negative control cells. In conclusion, using digital droplet polymerase chain reaction to follow the effect of host gene knockdown on virus replication is possible as long as the initial gene expression is high enough.
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(2022)The increasing use of antimicrobials causes a heavy pollution load on the environment and can enhance antimicrobial resistance of pathogenic bacteria, thus having a negative impact on human and animal health. Antibiotic concentrations in the environment are constantly monitored, however traditional chemical analyses fail to provide data on the bioavailability of antimicrobials. Whole-cell bacterial bioreporters have been developed to detect a wide variety of environmental pollutants including antimicrobials. These living, genetically engineered organisms can also be used for the measurement of the bioavailable fraction in a sample and thus bioreporters could give insights on the role of antimicrobial pollution in the dissemination of antimicrobial resistance. The aim of this study was to design and construct an improved bioluminescent bioreporter for detection of macrolide antibiotics. The mrx gene and the mph(A)R repressor gene were coupled with the mph(A) promotor of the macrolide resistance operon mph(A) and the reporter genes of the luciferase operon luxCDABE. The main objective was to determine whether Mrx, the hydrophobic and putative transmembrane transport protein of the macrolide resistance operon mph(A), would improve the sensitivity and reduce the induction time. Another aim was to optimize the use of three existing bioreporters with other macrolides than erythromycin, which was used earlier in testing their performance. The mrx-mph(A)R fragment was cloned into the pmph(A)luxCDABE vector, and the bioreporter plasmid was introduced to Escherichia coli strain DH10B. After verification of the construct pmph(A)luxCDABE-mrx-mph(A)R, the usability of the new whole-cell biosensor was compared against the three existing macrolide bioreporters with three different macrolide and lincosamide antibiotics, erythromycin, tylosin and clindamycin. The cloning of the new bioluminescent bioreporter for macrolides was performed successfully. However, the addition of erythromycin, tylosin or clindamycin to a suspension of E. coli DH10B(pmph(A)luxCDABE-mrx-mph(A)R) did not stimulate the expression of the lux genes. High concentrations of all three antibiotics triggered a light response with the existing bioreporters although the response was slow. The results indicated that further studies on the mrx gene and its encoded Mrx protein are still needed. The response of the mph(A) operon to other macrolide and lincosamide antibiotics than erythromycin was a positive and encouraging finding, since this enables detection of other synthetic macrolides than erythromycin as well as lincosamides with the existing bioreporters after optimization.
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(2016)Optimization of contrast enhanced CT (computed tomography) of the intra-abdominal lymphatic system in the case of a chylous leakage is the subject of the study. The chylous leakage means a pathologic condition, where the lymphatic liquid (chyle) leaks out from the vessels of the lymphatic system in intra-abdominal space. The diagnose is rare. CT imaging is based on a different attenuation of the X-rays when they are penetrating through tissues of different kind. Tissues with greater density, like iodine, make the attenuation stronger and they can be used to improve the contrast in the image. Iodinated contrast enhancing agent Lipiodol was chosen for this study for increasing contrast in the CT images of the intestines. The right ratio of the Lipiodol–oil mixing was searched so that the agent would end up in the lymphatic system. The idea was to visualize the lymphatic system and spot the leakage point. This could be useful information when thinking about the follow-up treatment, especially in the case of surgical operation. The examinations were implemented by imaging plastic phantoms with CT device. The CT images were taken with head and torso phantoms, including different mixing ratios of Lipiodol–oil mixtures. The most suitable mixing ratio of Lipiodol and oil was then estimated from the taken phantom pictures. After that, the results were taken in use with two chylous leakage patients, a 70-yearold male patient and a pediatric patient. The CT images of the patients were analysed with ImageJ program. The contrast enhancement when using the Lipiodol contrast enhancing agent was excellent, about 300-400 HU with 120 kV tube voltage. The suitable mixing ratio of the Lipiodol–oil mixture was estimated to be 1:8 with the adult patient and 1:10 with the pediatric patient. The leakage point could not be localized from the CT images. Reason for that might have been the image timing with the pediatric patient. She might have an exceptional rate of fat metabolism, because of her inborn malformations of the intestines. The biokinetical variations and variability of the mixing ratio in the different parts of the intestines also increase the uncertainty of the results of the study. The basic principle of Lipiodol as the contrast enhancing agent has now been tested and the properties of it have been found suitable for similar visualization examinations. The protocol for chylous leakage imaging can be developed and tested further when suitable patients will appear.
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(2020)Biomimetic native nanofibrillated cellulose (NFC) hydrogel has recently proven its efficacy, safety and diversity at the site of pharmaceutical industry. Yet, properties for the long-term storage in dry condition at room temperature and feasible transportation needs to be developed for NFC hydrogel before it is suitable for freeze-dried biomedical applications. Our aim was to optimize freeze-drying cycle for NFC hydrogel formulation with suitable lyoprotective biomolecules and preserve its properties after freeze-drying process and reconstitution. NFC hydrogel formulations with different combinations of chosen biomolecules were freeze-dried, and physicochemical properties and rheological features were characterized. In addition, morphology of the freeze-dried cakes was studied. The effects of the biomolecules on the water contents in NFC systems were simulated for both of the crystal and amorphous ones. All the results of the characteristics were compared with the non-freeze-dried NFC hydrogel formulations. NFC hydrogel formulation, which had the most optimal preservation properties after freeze-drying and reconstitution, was optimized. We hypothesized that without any chemical modifications native NFC hydrogel can be successfully freeze-dried and subsequently reconstituted with the proper biomolecules only by using biological and natural materials, which are human and xenon-free for the further use in biomedical applications of the native NFC hydrogel.
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(2018)Human gut microbiota is an important topic for many different disciplines. Various factors, e.g. antimicrobial drugs and diet, affect the development and balance of gut microbiota and its interactions with the host. Plant based carbohydrates that transit unabsorbed and undigested through the upper parts of gastrointestinal tract are an important source of energy for the colon bacteria. Some of colon bacteria produce short chained fatty acids (e.g. acetate, propionate, butyrate) from these carbohydrates. SCFAs provide a source of energy and regulate the cell growth and metabolism. The changes in the diversity and abundance of the SCFA producing bacteria have been linked to many gut related diseases. Studying gut microbiota with today’s analytical methods is still challenging. In this work the effects of dietary fibers on gut microbiota were monitored with a static, single vessel batch model. A batch model is typically developed for the quick high-throughput screening of samples. Fiber samples were processed in various ways to increase their solubility and thus fermentability. In this work butyrate producing bacteria, Akkermansia muciniphila and bifidobacteria were targeted. Enumeration was performed with selective growth media and quantitative PCR. Bacterial population was characterized by 16S rRNA based sequencing. To quantitate only viable bacterial cells from the sample matrix by qPCR, samples were treated with propidium monoazide (PMA), which after light activation inhibits the amplification of double-stranded DNA from dead and lysed cells. Since acidic SCFAs accumulate in the sample suspension, pH decreases clearly during the incubation in the static model. This leads to conditions which do not resemble the ones in the colon. Two different buffer solutions, pH adjustment and shorter incubation time were tested to overcome this challenge. The numbers of A. muciniphila and some of the butyrate producers decreased in acidic environment and the proportion of acid-tolerant bacteria was clearly increased and dominated the bacterial population. The optimization of PMA treatment for fecal suspension samples proved to be challenging due to the highly variable composition of sample matrixes. Dietary fibers were observed to cause different changes in bacterial population: the most soluble fibers caused greater decrease of pH and thus greater proportion of acid tolerant bacteria in the population.
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(2016)There is a growing interest towards continuous manufacturing in pharmaceutical industry. When considering solid dosage form manufacturing and continuous wet granulation, twin screw granulation is the most studied technology. In spite of this, process knowledge is not as comprehensive as it is for batch granulation technologies such as high shear granulation. One problem with twin screw granulation seems to be bimodal and broad particle size distribution of granules. Specific causes of bimodal distribution and the ways to possibly gain unimodality either in granulation step or via dry milling are not fully understood. The purpose of this study was to optimize the ConsiGma25 continuous twin screw wet granulation process and study dry milling as a possible way of gaining unimodal particle size distribution in order to optimize particle size for tablet compression purposes. One aim was also to compress tablets from the obtained twin screw granules and evaluate the quality against high shear and direct compressed tablets of same formulation. Central composite circumscribed design was used as a design of experiments for twin screw wet granulation process. Factors (powder feed rate, screw speed, liquid to solid ratio (L/S ratio) and mill screen size) were varied in two levels. In total, 29 experiments were conducted. Tablet compression design was fractional as only 11 experiments from the twin screw granulation design were tableted. High shear granulation was conducted with Diosna P-1/6 using three different L/S ratios. All of these batches were compressed to tablets. Also direct compression was carried out. Formulation used had ibuprofen as active pharmaceutical ingredient, mannitol and MCC as fillers, HPC as binder and croscarmellose sodium as disintegrant. Lubricant, sodium stearyl fumarate, was blended to granules before tablet compression. Torque was measured during granulation in order to evaluate equilibration of the twin screw granulation process. It stabilized quickly and stayed stable after parameter changes and increased as L/S ratio and barrel fill rate increased. Particle size distribution and flowability of granules were analysed and tablets were analysed according to European and United States pharmacopoeias. Also tensile strengths and compactibilities were evaluated. Particle size distributions of unmilled twin screw granules were bimodal and broad. After dry milling, QicPic dynamic image analysis results showed unimodal particle size distributions for all experiments whereas Mastersizer laser diffraction analysis showed more unimodal distributions for experiments milled with smaller mill screen sizes. Mill screen size had the largest effect on particle size and as increased mill screen size increased particle size. Results showed that dry milling was a way to optimize particle size distribution for tablet compression purposes. Also flowability of formulation and process parameters needed to be optimized as granulation parameters had an effect on particle size and manufacturability was enhanced with better flowing formulation compared to previous study. Knowledge of the influence of L/S ratio, screw speed and powder feed rate, on granule size was gained. The effect of these process parameters varied depending whether d10, d50 or d90 was measured and particle size analysis method used. Increased L/S ratio and screw speed increased granule size as increased powder feed rate decreased it. Twin screw tablets showed higher tensile strengths and better compactibility compared to both high shear tablets and direct compressed tablets. Twin screw tablets showed also faster dissolution compared to direct compressed tablets probably due to of lower compression force. Mill screen size had the largest effect on dissolution properties of the twin screw tablets. When larger mill screen size was used, dissolution was slower due to larger particle size. Also increased powder feed rate made dissolution rate slower due to higher fill rate of the barrel. In other tablet properties analysed, no significant differences were seen between different twin screw experiments or between twin screw tablets and direct compressed tablets. All of the twin screw tablets and direct compressed tablets fulfilled the requirements of European and United states pharmacopoeia. As a conclusion, continuous granulation process was successfully optimized and high quality tablets resulted showing especially the effect of dry milling on granule size and shape as well as on tablet properties.
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Optimization of sample preparation for next-generation sequencing with Illumina Genome Analyzer II (2010)The growing interest for sequencing with higher throughput in the last decade has led to the development of new sequencing applications. This thesis concentrates on optimizing DNA library preparation for Illumina Genome Analyzer II sequencer. The library preparation steps that were optimized include fragmentation, PCR purification and quantification. DNA fragmentation was performed with focused sonication in different concentrations and durations. Two column based PCR purification method, gel matrix method and magnetic bead based method were compared. Quantitative PCR and gel electrophoresis in a chip were compared for DNA quantification. The magnetic bead purification was found to be the most efficient and flexible purification method. The fragmentation protocol was changed to produce longer fragments to be compatible with longer sequencing reads. Quantitative PCR correlates better with the cluster number and should thus be considered to be the default quantification method for sequencing. As a result of this study more data have been acquired from sequencing with lower costs and troubleshooting has become easier as qualification steps have been added to the protocol. New sequencing instruments and applications will create a demand for further optimizations in future.
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Optimization of the CMS high level trigger for low mass supersymmetry searches with forward protons (2020)The Standard Model (SM) is the best established theory describing the observed matter and its interactions through all the fundamental forces except gravity. The SM is however not complete. For example, it does not explain the large difference between the electroweak scale and the Planck scale, which is known as the hierarchy problem, nor does it explain dark matter. Therefore there is a need for more comprehensive theories beyond the SM. Supersymmetry (SUSY) extends the SM with predictions of a partner particle (sparticle) for each currently known elementary particle. A few of its benefits are that it gives an explanation to the hierarchy problem and predicts the existence of a good particle candidate for dark matter. However, there is no experimental evidence for SUSY so far. The search for SUSY particles is currently on-going at the experiments using the Large Hadron Collider (LHC) at CERN. So far, the searches have been focusing on strongly interacting supersymmetric particles, still without findings. One of the parameter ranges still to be covered, is the compressed mass scenario in the lower mass end for weakly interacting sparticles, where the masses of the lightest and second lightest supersymmetric particle do not differ much in mass. If they exist, low mass SUSY particles could be created in the LHC from two fusing photons emitted by forward-scattered protons. In such two-photon (central exclusive) processes, both protons might remain on-shell and continue their path down the beamline. Central exclusive processes are rather rare, so to advance the study of these events, new tagging techniques are required to record as many of these events as possible. We are interested in the kinematic range with a mass difference of less than 60 GeV between the slepton and the neutralino, which are the supersymmetric partners of the lepton and the neutral bosons. The CMS detector in the LHC has two event filtering (trigger) systems; the low level (L1) trigger and the high level trigger (HLT). A study has been conducted on how a specific HLT could increase the number of recorded events for the previously mentioned process, without significantly increasing the total HLT rate. To select more events, the transverse momentum threshold value of the produced leptons ought to be lowered. The forward-scattered protons will be detected by the Precision Proton Spectrometer (PPS). This thesis shows that requiring proton tracks in the PPS tracking detectors and tuning the multiplicity cut of these, will compensate for the lowering of the transverse momentum threshold, keeping the overall HLT rate sensible, while still enabling more interesting physics to be recorded.
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Optimization of VIGS and functional analysis of Gerbera hybrida TCP genes in Calendula officinalis (2012)The evolution of floral novelties involves activities of several transcription factors. The large Asteraceae plant family has inflorescences consisting of different types of flowers. TCP transcription factors have recently been reported to regulate this complex structure. Gerbera hybrida, a common ornamental crop, has been used as a model plant for flower developmental studies in Asteraceae. It can be genetically transformed; however, transformation is laborious and time-consuming. Calendula officinalis also belongs to the Asteraceae plant family. It has working micropropagation methods, and it grows and flowers faster than Gerbera hybrida. In addition, Calendula officinalis genes possess high sequence similarity to Gerbera hybrida genes and thus provide an opportunity for functional testing of large numbers of genes. For functional assessment, virus induced gene silencing (VIGS) is a rapid approach, as it circumvents the need to establish stable transgenic lines that requires efficient tissue culture and time-consuming whole-plant regeneration steps. In this study, twelve Calendula officinalis cultivars were tested for VIGS. Calendula showed potential as a new model for the Asteraceae plant family as all twelve different cultivars could be infected by tobacco rattle virus (TRV) via observing the fluorescence caused by pTRV2: GFP; and they all showed photobleaching silencing phenotype caused by PHYTOENE DESATURASE (GhPDS) gene from gerbera. Especially the cultivars „Touch of Red/Orange? and „Princess Orange? turned out to be the most efficient in silencing. Virus dynamics was successfully traced by fluorescence encoded by pTRV2: GFP construct. However, using the construct pTRV2: GFP: PDS, it was observed that the GFP gene could not be applied as a marker gene to indicate the silencing area, because fluorescence could not be observed in photobleaching area. The calendula PDS was also tested. More similar sequence corresponding to the plant?s endogenous gene could cause more visible silencing symptom, but quantitative polymerase chain reaction results showed no statistically significant difference on gene silencing efficiency between GhPDS and CoPDS fragments. VIGS was also tested for silencing of TCP domain transcription factor genes using gerbera specific gene fragments. It was observed that the VIGS approach was not suitable for functional testing of CYCLOIDEA-clade genes in Calendula officinalis as identification of the putative phenotypes was highly disturbed by variable inflorescence phenotype of the tested cultivar.
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(2020)The aim of this thesis was to create an optimized bioprocessing to solubilize the maximal amount of proteins from the wheat bran without losing their nutritional and technological quality. The hypothesis of this thesis was that a maximal degradation of the aleurone cell wall components would lead to a maximal amount of soluble proteins originally located inside the aleurone layer. The literature review further looked into possible extraction methods for wheat bran proteins. Fine wheat bran was chosen to be bioprocessed by using experimental design to find optimal conditions for protein solubilization. Bioprocessing was done either by using starter culture alone or a combination of selected enzymes and starter culture. Independent studied factors were time (8 h, 16 h, 24 h), temperature (20 °C, 27.5 °C, 35 °C) and enzyme dosage (5 nkat/g, 50 nkat/g, 500 nkat/g). Optimization was carried out by applying response surface methodology to analyze the relationship between the response and the independent variables. Optimized bioprocessing of wheat bran led to maximal protein solubilization of >50% for wheat bran both bioprocessed with starter culture and with starter culture and enzymes after fermentation time of 24 h. Thus, the amount of soluble protein increased 23%. This indicated that the use of enzymes did not improve the breaking down of the aleurone cell walls for protein liberation. Furthermore, the use of enzymes affected heavily the protein degradation for fermentations longer than 8 h. Since the amount of solubilized protein was higher for wheat bran bioprocessed for 8 h with starter only (>46%) than for wheat bran bioprocessed for 8 h with starter and enzymes (>40%), the use of enzymes for a larger scale production does not seem feasible.
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