Particle detector link system modifications in RE1/1 sector

The large hadron collider constructed at the European organization for nuclear research, CERN, is the world’s largest single measuring instrument ever built, and also currently the most powerful particle accelerator that exists. The large hadron collider includes six different experiment stations, one of which is called the compact muon solenoid, or the CMS. The main purpose of the CMS is to track and study residue particles from proton-proton collisions. The primary detectors utilized in the CMS are resistive plate chambers (RPCs). To obtain data from these detectors, a link system has been designed. The main idea of the link system is to receive data from the detector front-end electronics in parallel form, and to transmit it onwards in serial form, via an optical fiber. The system is mostly ready and in place. However, a problem has occurred with innermost RPC detectors, located in sector labeled RE1/1; transmission lines for parallel data suffer from signal integrity issues over long distances. As a solution to this, a new version of the link system has been devised, a one that fits in smaller space and can be located within the CMS, closer to the detectors. This RE1/1 link system has been so far completed only partially, with just the mechanical design and casing being done. In this thesis, link system electronics for RE1/1 sector has been designed, by modifying the existing link system concept to better meet the requirements of the RE1/1 sector. In addition to completion of the prototype of the RE1/1 link system electronics, some testing for the system has also been done, to ensure functionality of the design.

Integration of a Bioethanol Process to a Pulp Mill

Tässä diplomityössä tutkittiin puuhakkeen esihydrolyysi- ja hakkuujätteen hydrolyysiprosessien integroimista sellutehtaaseen bioetanolin tuottamiseksi. Tällaisesta ns. biojalostamosta luotiin WinGEMS-simulointiohjelmalla simulointimalli, jonka avulla tutkittiin bioetanoliprosessin vaikutusta sellutehtaan massa- ja energiataseisiin sekä alustavaa biojalostamon kannattavuutta. Simuloinnissa tarkasteltiin kolmea eri tapausta, joissa mäntysellun tuotannon ajateltiin olevan 1000 tonnia päivässä ja hakkuujätettä käytettävän 10 % tarvittavan kuitupuun määrästä: 1) Puuhakkeen esihydrolyysi ja hakkuujätteen hydrolyysi etanolin tuottamiseksi 2) Puuhakkeen esihydrolyysi, hakkuujäte kuorikattilaan poltettavaksi 3) Ei esihydrolyysiä, hakkuujäte kuorikattilaan poltettavaksi Verrattuna tapaukseen 3, puun kulutus kasvaa 16 % esihydrolysoitaessa puuhake ennen keittoa tapauksissa 1 ja 2. Kasvaneella puun kulutuksella tuotetaan tapauksessa 1 149 tonnia etanolia ja 240 MWh enemmän ylimääräsähköä päivässä. Tapauksessa 2 tuotetaan 68 tonnia etanolia ja 460 MWh enemmän ylimääräsähköä päivässä. Tämä tuottaisi vuotuista lisäkassavirtaa 18,8 miljoonaa euroa tapauksessa 1 ja 9,4 miljoonaa euroa tapauksessa 2. Hydrolyysin tuoteliuoksen, hydrolysaatin, haihduttaminen sekä hydrolyysiprosessien orgaanisten jäännöstuotteiden haihduttaminen ja polttaminen kasvattavat haihduttamon ja soodakattilan kuormitusta. Verrattuna tapaukseen 3, tapauksissa 1 ja 2 haihduttamon vaiheiden määrä on kasvatettava viidestä seitsemään ja tarvittavat lämmönsiirtopinta-alat lähes kaksinkertaistettava. Soodakattilan kuormitus kasvaa 39 % tapauksessa 1 ja 26 % tapauksessa 2.

Hakkeen kuivaus ennen varastointia ja biopolttoaineterminaalin suunnittelu

Lempäälään aiotaan rakentaa uusi kaukolämpölaitos, jossa polttoaineena käytettäisiin haketta. Nykyään Lempäälässä tuotetaan kaukolämpöä maakaasulla, jonka käyttämisestä halutaan siirtyä käyttämään lähialueilta saatavaa biopolttoainetta. Tässä työssä halutaan selvittää, mitä hyötyjä saataisiin hakkeen koneellisesta kuivauksesta. Työn toisena tavoitteena on suunnitella ja pohtia biopolttoaineterminaalin rakentamista sekä käsitellä hakkeen varastointia yleensä. Työssä tutustutaan hakkeeseen aiheesta kertovan kirjallisuuden avulla. Työssä on myös laskettu hakkeen kuivauksesta saatavia hyötyjä hakkeen lämpöarvoon sekä energiatiheyteen. Erityisesti perehdytään metsätähdehakkeeseen, rankahakkeeseen, kuorihakkeeseen sekä sahanpuruun. Laskelmien tuloksista on havaittu, että suurin hyöty hakkeen energiatiheyden parantumisessa saadaan kun hake kuivataan 35 % kosteuspitoisuuteen. Tämän jälkeen energiatiheyden paraneminen tapahtuu hitaammin. Hakkeen kuivauksesta saadaan myös muita hyötyjä kuin energiatiheyden paraneminen. Kuivan hakkeen käsittelyn ja varastoinnin on havaittu olevan vaivattomampaa kuin märän hakkeen. Biopolttoaineterminaalin ja voimalaitoksen tulisi sijaita rinnakkain, jotta hakkeen kuivauksesta saadaan mahdollisimman kustannustehokasta. Näin ollen syntyisi myös säästöjä hakkeen kuljetuksen suhteen. Biopolttoaineterminaalin rakentamista varten tarvittaisiin tilaa alustavien laskelmien perusteella noin yksi hehtaari. Työssä on myös laskettu biopolttoaineterminaalin rakentamisesta aiheutuvia kustannuksia sekä hakkeen kuljetuksesta koituvia logistiikka kustannuksia. Haketerminaalin ja voimalaitoksen sijaintia Lempäälässä on myös kartoitettu.

Biocide analysis, usability and stability

Biosidien toimittajat tavallisesti suorittavat biosidien annostelumäärien hallinnan paperi- ja kartonkiteollisuudessa. Useimmiten annostelun hallinta määritetään epäsuorilla menetelmillä, kuten esimerkiksi määrittämällä bakteerien kasvua. Biosidien tehoaineiden todellista konsentraatiota tai määrää prosessivesissä tai lopputuotteessa ei tavallisesti mitata. Diplomityössä kehitettiin kolmelle paperiteollisuudessa yleisesti käytetyllä biosidin tehoaineelle analyyttiset menetelmät. Menetelmät kehitettiin glutaraldehydille, 2,2-dibromi-3-nitriilipropionamidi:lle (DBNPA) ja 5-kloori-2-metyyli-4-isotiatsoliini-3-oni:lle (CMI). Kehitettyjä menetelmiä käytettiin tehoaineiden stabiilisuuden seuraamiseen vesiliuoksessa eri pH:ssa ja lämpötilassa. Lisäksi kartonkinäytteistä tehtiin uuttokokeita ja yritettiin kehittää uuttomenetelmät, joilla pystyttäisiin määrittämään biosidien tehoaineiden jäännöspitoisuuksia lopputuotteesta. Glutaraldehydille ja CMI:lle onnistuttiin kehittämään uuttomenetelmät, joilla pystyttiin määrittämään kartongista tutkittujen tehoaineiden jäännöspitoisuudet. Saadut tulokset vaikuttavat realistisilta. Glutaraldehydille ja DBNPA:lle tehtiin stabiilisuuskokeita ja tulokset ovat samankaltaisia mitä muut tutkijat ovat saaneet.

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.

Characterisation of Human Neutral and Lysosomal alpha-Mannosidases

Neutral alpha-mannosidase and lysosomal MAN2B1 alpha-mannosidase belong to glycoside hydrolase family 38, which contains essential enzymes required for the modification and catabolism of asparagine-linked glycans on proteins. MAN2B1 catalyses lysosomal glycan degradation, while neutral α-mannosidase is most likely involved in the catabolism of cytosolic free oligosaccharides. These mannose containing saccharides are generated during glycosylation or released from misfolded glycoproteins, which are detected by quality control in the endoplasmic reticulum. To characterise the biological function of human neutral α-mannosidase, I cloned the alpha-mannosidase cDNA and recombinantly expressed the enzyme. The purified enzyme trimmed the putative natural substrate Man9GlcNAc to Man5GlcNAc, whereas the reducing end GlcNAc2 limited trimming to Man8GlcNAc2. Neutral α-mannosidase showed highest enzyme activity at neutral pH and was activated by the cations Fe₂+, Co2+ and Mn₂+, Cu2+ in turn had a strong inhibitory effect on alpha-mannosidase activity. Analysis of its intracellular localisation revealed that neutral alpha-mannosidase is cytosolic and colocalises with proteasomes. Further work showed that the overexpression of neutral alpha-mannosidase affected the cytosolic free oligosaccharide content and led to enhanced endoplasmic reticulum associated degradation and underglycosylation of secreted proteins. The second part of the study focused on MAN2B1 and the inherited lysosomal storage disorder α-mannosidosis. In this disorder, deficient MAN2B1 activity is associated with mutations in the MAN2B1 gene. The thesis reports the molecular consequences of 35 alpha-mannosidosis associated mutations, including 29 novel missense mutations. According to experimental analyses, the mutations fall into four groups: Mutations, which prevent transport to lysosomes are accompanied with a lack of proteolytic processing of the enzyme (groups 1 and 3). Although the rest of the mutations (groups 2 and 4) allow transport to lysosomes, the mutated proteins are less efficiently processed to their mature form than is wild type MAN2B1. Analysis of the effect of the mutations on the model structure of human lysosomal alpha-mannosidase provides insights on their structural consequences. Mutations, which affect amino acids important for folding (prolines, glycines, cysteines) or domain interface interactions (arginines), arrest the enzyme in the endoplasmic reticulum. Surface mutations and changes, which do not drastically alter residue volume, are tolerated better. Descriptions of the mutations and clinical data are compiled in an α-mannosidosis database, which will be available for the scientific community. This thesis provides a detailed insight into two ubiquitous human alpha-mannosidases. It demonstrates that neutral alpha-mannosidase is involved in the degradation of cytosolic oligosaccharides and suggests that the regulation of this α-mannosidase is important for maintaining the cellular homeostasis of N-glycosylation and glycan degradation. The study on alpha-mannosidosis associated mutations identifies multiple mechanisms for how these mutations are detrimental for MAN2B1 activity. The α-mannosidosis database will benefit both clinicians and scientific research on lysosomal alpha‑mannosidosis.

Probing MST1 Kinase Sequence and Structure for Rational Drug Discovery (Targeting diabetes by blocking protein-protein interactions)

Apoptotic beta cell death is an underlying cause majorly for type I and to a lesser extent for type II diabetes. Recently, MST1 kinase was identified as a key apoptotic agent in diabetic condition. In this study, I have examined MST1 and closely related kinases namely, MST2, MST3 and MST4, aiming to tackle diabetes by exploring ways to selectively block MST1 kinase activity. The first investigation was directed towards evaluating possibilities of selectively blocking the ATP binding site of MST1 kinase that is essential for the activity of the enzymes. Structure and sequence analyses of this site however revealed a near absolute conservation between the MSTs and very few changes with other kinases. The observed residue variations also displayed similar physicochemical properties making it hard for selective inhibition of the enzyme. Second, possibilities for allosteric inhibition of the enzyme were evaluated. Analysis of the recognized allosteric site also posed the same problem as the MSTs shared almost all of the same residues. The third analysis was made on the SARAH domain, which is required for the dimerization and activation of MST1 and MST2 kinases. MST3 and MST4 lack this domain, hence selectivity against these two kinases can be achieved. Other proteins with SARAH domains such as the RASSF proteins were also examined. Their interaction with the MST1 SARAH domain were evaluated to mimic their binding pattern and design a peptide inhibitor that interferes with MST1 SARAH dimerization. In molecular simulations the RASSF5 SARAH domain was shown to strongly interact with the MST1 SARAH domain and possibly preventing MST1 SARAH dimerization. Based on this, the peptidic inhibitor was suggested to be based on the sequence of RASSF5 SARAH domain. Since the MST2 kinase also interacts with RASSF5 SARAH domain, absolute selectivity might not be achieved.