Aikaerotteisesti fluoresenssia mittaavan reaaliaikaisen PCR-laitteen kehitys

Kvantitatiivinen reaaliaikainen polymeraasiketjureaktio (engl. polymerase chain reaction, PCR) on osoittautunut käyttäjäystävällisimmäksi menetelmäksi nukleiinihapposekvenssien kvantitoimisessa. Tätä menetelmää voidaan herkistää pienempien DNA-pitoisuuksien havaitsemiseen käyttämällä hyväksi aikaerotteista fluorometriaa (engl. time-resolved fluorometry, TRF) ja luminoivia lantanidileimoja, joiden fluoresenssin pitkän eliniän ansiosta emission mittaus voidaan suorittaa vasta hetki virittävän valopulssin jälkeen, jolloin lyhytikäinen taustasäteily ehtii sammua. Tuloksena saadaan korkea signaali-taustasuhde. Tämän diplomityön tarkoituksena oli rakentaa TRF:än pystyvä reaaliaikainen PCR-laite, sillä tällaista laitetta ei ole markkinoilla tarjolla. Laite rakennettiin kehittämällä lämpökierrätin ja yhdistämällä se valmiiseen TRF:än kykenevään mittapäähän. Mittapään ja lämpökierrättimen hallitsemiseksi kehitettiin myös tietokoneohjelma. Valon tuottamiseksi ja mittaamiseksi haluttiin käyttää edullisia komponentteja, joten työssä käytettiin valmiin mittapään optiikkaa, jossa viritys tapahtuu hohtodiodilla (engl. light-emitting diode, LED) ja lantanidileiman emission mittaus fotodiodilla (engl. photodiode, PD) tai valomonistinputkella (engl. photomultiplier tube, PMT). Myös mittapään suorituskykyä tutkittiin. Työtä varten kehitettiin lämpökierrätin, joka koostui Peltier-elementillä lämmitettävästä PCR-putkitelineestä ja lämpökannesta. Mittalaitteen suorituskyvyn tutkimiseen käytettiin kelaattikomplementaatioon perustuvaa PCR-tuotteen havaitsemismenetelmää. Kelaattikomplementaatio perustuu kahteen erilliseen oligonukleotidimolekyyliin, joista toiseen on sidottu lantanidi-ioni ja toiseen valoa absorboiva ligandirakenne, jotka yhdessä muodostavat fluoresoivan kokonaisuuden. Kehitetyn lämpökierrättimen todettiin olevan tarpeeksi tarkka sekä tehokas ja sen lämmitys- ja jäähdytysnopeuden maksimeiksi saatiin 2,6 °C/sekunti. Detektorina käytetyn PD:n ei todettu olevan tarpeeksi herkkä emission havainnoimiseksi ja se korvattiin laitteessa PMT:llä. Käytetyllä PCR-määrityksellä kynnyssykleiksi (engl. threshold cycle, Ct) sekä kehitetylle että referenssilaitteelle saatiin 28,4 käyttämällä samaa 100 000 kopion DNA:n aloitusmäärää. Työssä osoitettiin, että on mahdollista kehittää edullisia komponentteja käyttävä, TRF:än pystyvä, reaaliaikainen PCR-laite, joka kykenee vastaavaan Ct-arvoon kuin vertailulaite. PD:n herkkyys ei kuitenkaan riittänyt. Tulokset olivat lupaavia, sillä LED- ja PD-teknologiat kehittyvät ja markkinoille on tullut myös muita komponentteja, joiden avulla on tulevaisuudessa mahdollista kehittää vielä herkempi laite.

Couplets pour le mariage de Monseigneur le Dauphin, et de Madame la Dauphine par. M. J. D. Bezassier, chanoine régulier de l'abbaye de Saint-Loup de Troyes / par. M. J. D. Bezassier, chanoine régulier de l'abbaye de Saint-Loup de Troyes ; [exemplaire illustré par Gabriel de Saint-Aubin]

Référence bibliographique : Dacier 1931a, 1067

Expression and function of endothelin and its receptors in vascular adventitial fibroblasts

Objective: The adventitia has been recognized to play important roles in vascular oxidative stress, remodelling and contraction. We recently demonstrated that adventitial fibroblasts are able to express endothelin-1 (ET-1) in response to angiotensin II (ANG II). However, the mechanisms by which ANG II induces ET-1 expression are unknown. It is also unclear whether the ET-1 receptors are expressed in the adventitia. We therefore examined the role of oxidative stress in the regulation of ET-1. We also investigated the expression of both the ETA and ETB receptors and the roles of these two types of receptors in collagen synthesis and ET-1 clearance in adventitial fibroblasts. Methods and Results: Adventitial fibroblasts were isolated and cultured from the thoracic mouse aorta. Cells were treated with ANG II (lOOnM), ET-1 (lOpM), NADPH oxidase inhibitor apocynin (lOOfiM), the superoxide anion scavenger tempol (lOOfiM), the ANG II receptor antagonists (100[aM), losartan (AT| receptor) and PD 1233 19 (AT2 receptor), the ET-1 receptor antagonists (lOOuM), BQ123 (ETA receptor) and BQ788 (ETB receptor), and the ETB receptor agonist (lOOnM) Sarafotoxin 6C. ET-1 peptide levels were determined by ELISA, while ETA ,ETB and collagen levels were determined by Western blot. ANG II increased ET-1 peptide levels in a time-dependent manner reaching significance when incubated for 24 hours. NAD(P)H oxidase inhibitor, apocynin, as well as the superoxide scanverger, tempol, significantly reduced ANG Il-induced ET-1 peptide levels while over-expression of SOD1 (endogenous antioxidant enzyme) significantly decreased ANG Il-induced collagen I expression, therefore implicating reactive oxygen species in the mediation of ET-1. ANG II increased ETA receptor protein as well as collagen in a similar fashion, reaching significance after 4, 6, and 24 hours treatment. ANG II induced collagen was reduced while in the presence of the ETA receptor antagonist suggesting the role of the ETa receptor in the regulation of the extracellular matrix. ANG II treatment also increased ETB receptor protein levels in a time-dependent manner. ANG II treatment in the presence of the ETB receptor antagonist significantly increased ET-1 peptide levels. On another hand, the ETB receptor agonist, Sarafotoxin 6C, significantly decreased ET-1 peptide levels. These data implicate the role of the ETb receptor in the clearance of the ET-1 peptide. Conclusion: ANG II-induced increases of ET-1 peptide appears to be mediated by reactive oxygen species derived from NAD(P)H oxidase. Both the ETA and ETB receptors are expressed in adventitial fibroblasts. The ETA receptor subtype mediates collagen I expression, while the ETB receptor may play a protective role through increasing the clearance of the ET- 1 peptide.

Reactivity characteristics of cytochrome c, cytochrome oxidase and the electrostatic cytochrome c - cytochrome oxidase complex /

The mechanism whereby cytochrome £ oxidase catalyses elec-. tron transfer from cytochrome £ to oxygen remains an unsolved problem. Polarographic and spectrophotometric activity measurements of purified, particulate and soluble forms of beef heart mitochondrial cytochrome c oxidase presented in this thesis confirm the following characteristics of the steady-state kinetics with respect to cytochrome £: (1) oxidation of ferrocytochrome c is first order under all conditions. -(2) The relationship between sustrate concentration and velocity is of the Michaelis-Menten type over a limited range of substrate. concentrations at high ionic strength. (3) ~he reaction rate is independent from oxygen concentration until very low levels of oxygen. (4) "Biphasic" kinetic plots of enzyme activity as a function of substrate concentration are found when the range of cytochrome c concentrations is extended; the biphasicity ~ is more apparent in low ionic strength buffer. These results imply two binding sites for cytochrome £ on the oxidase; one of high affinity and one of low affinity with Km values of 1.0 pM and 3.0 pM, respectively, under low ionic strength conditions. (5) Inhibition of the enzymic rate by azide is non-c~mpetitive with respect to cytochrome £ under all conditions indicating an internal electron transfer step, and not binding or dissociation of £ from the enzyme is rate limiting. The "tight" binding of cytochrome '£ to cytochrome c oxidase is confirmed in column chromatographic experiments. The complex has a cytochrome £:oxidase ratio of 1.0 and is dissociated in media of high ionic strength. Stopped-flow spectrophotometric studies of the reduction of equimolar mixtures and complexes of cytochrome c and the oxidase were initiated in an attempt to assess the functional relevance of such a complex. Two alternative routes -for reduction of the oxidase, under conditions where the predominant species is the £ - aa3 complex, are postulated; (i) electron transfer via tightly bound cytochrome £, (ii) electron transfer via a small population of free cytochrome c interacting at the "loose" binding site implied from kinetic studies. It is impossible to conclude, based on the results obtained, which path is responsible for the reduction of cytochrome a. The rate of reduction by various reductants of free cytochrome £ in high and low ionic strength and of cytochrome £ electrostatically bound to cytochrome oxidase was investigated. Ascorbate, a negatively charged reagent, reduces free cytochrome £ with a rate constant dependent on ionic strength, whereas neutral reagents TMPD and DAD were relatively unaffected by ionic strength in their reduction of cytochrome c. The zwitterion cysteine behaved similarly to uncharged reductants DAD and TI~PD in exhibiting only a marginal response to ionic strength. Ascorbate reduces bound cytochrome £ only slowly, but DAD and TMPD reduce bound cytochrome £ rapidly. Reduction of cytochrome £ by DAD and TMPD in the £ - aa3 complex was enhanced lO-fold over DAD reduction of free £ and 4-fold over TMPD reduction of free c. Thus, the importance of ionic strength on the reactivity of cytochrome £ was observed with the general conclusion being that on the cytochrome £ molecule areas for anion (ie. phosphate) binding, ascorbate reduction and complexation to the oxidase overlap. The increased reducibility for bound cytochrome £ by reductants DAD and TMPD supports a suggested conformational change of electrostatically bound c compare.d to free .£. In addition, analysis of electron distribution between cytochromes £ and a in the complex suggest that the midpotential of cytochrome ~ changes with the redox state of the oxidase. Such evidence supports models of the oxidase which suggest interactions within the enzyme (or c - enzyme complex) result in altered midpoint potentials of the redox centers.

Phonon spectra and thermal properties of some fcc metals using embedded-atom potentials /

By employing the embedded-atom potentials of Mei et ai.[l], we have calculated the dynamical matrices and phonon dispersion curves for six fee metals (Cu,Ag,Au,Ni,Pd and Pt). We have also investigated, within the quasiharmonic approximation, some other thermal properties of these metals which depend on the phonon density of states, such as the temperature dependence of lattice constant, coefficient of linear thermal expansion, isothermal and adiabatic bulk moduli, heat capacities at constant volume and constant pressure, Griineisen parameter and Debye temperature. The computed results are compared with the experimental findings wherever possible. The comparison shows a generally good agreement between the theoretical values and experimental data for all properties except the discrepancies of phonon frequencies and Debye temperature for Pd, Pt and Au. Further, we modify the parameters of this model for Pd and Pt and obtain the phonon dispersion curves which is in good agreement with experimental data.

The impact of drug-induced dyskinesias on rapid alternating movements in patients with Parkinson's disease

We investigated the likelihood that hypokinesia/bradykinesia coexist with druginduced dyskinesias (DID) in patients with Parkinson's disease (PD). The influence of dyskinesias on rapid alternating movements (RAM) was investigated in ten dyskinetic patients (DPD). Their motor performance was compared to that of ten age/gendermatched non-dyskinetic patients (NDPD) and ten healthy control subjects. Whole-body magnitude (WBM) and fast pronation-supination at the wrist were recorded using 6- degrees of freedom magnetic motion tracker and forearm rotational sensors, respectively. Subjects were asked to pronate-supinate their dominant hand for 10s. Pre- and postmeasures were taken in a neutral position for 20s. RANGE (measure of hypokinesia), DURATION (measure of bradykinesia). VELOCITY (measure of bradykinesia) and IRREGULARITY (measure of fluctuations in movement amplitude) were used to assess RAM performance. Results showed that DPD patients had greater WBM than NDPD and control groups during rest and RAM performance. There were no differences in performance between NDPD and DPD groups for RANGE, DURATION and VELOCITY, despite significant longer disease duration for the DPD group (DPD = 15.5 ± 6.2 years versus NDPD = 6.6 ± 2.6 years). However, both the NDPD and DPD groups showed lower RANGE, longer DURATION, and reduced VELOCITY compared to controls,, suggesting the presence of bradykinesia and hypokinesia. In the case of IRREGULARITY, DPD patients showed clear fluctuations in movement amplitude compared to the NDPD and control groups. However, the lack of correlation between WBM and IRREGULARITY within the DPD group (Spearman's rank order, Rho - 0.31, p > 0.05), suggests that DID was not the primary cause of the fluctuating movementamplitude observed in that group. In conclusion, these findings suggest that DID may coexists with bradykinesia and hypokinesia, but that they are not inevitably accompanied with worsening motor performance.

Investigations into the determinations of hydride-forming elements

Analytical methods for the determination of trace amounts of germanium, tin and arsenic were established using hydride generation coupled with direct current plasma atomic emission spectrometry. A continuous gas flowing batch system for the hydride generation was investigated and was applied to the determination of germanium(Ge), tin(Sn), antimony(Sb) and lead(Pb) (Preliminary results suggest that it is also applicable to arsenic)As) ). With this system, the reproducibility of signals was improved and the determination was speeded up, compared with the conventional batch type hydride generation system. Each determination was complete within one minute. Interferences from a number of transition metal ions, especially from Pd(II), Pt(IV), Ni(II), Cu(II), Co(II), and Fe(II, III), have proven to be very serious under normal conditions, in the determination of germanium, tin, and arsenic. These interference effects were eliminated or significantly reduced in the presence of L-cystine or L-cysteine. Thus, a 10-1000 fold excess of Ni(II), Cu(II), Co(II), Fe(II), Pt(IV), Pd(II), etc. can be tolerated without interference, In the presence of L-cystine or L-cysteine, compared with absence of interference reducing agent. The methods for the determination of Ge, Sn, and As were examined by the analyses of standard reference materials. Interference effects from the sample matrix, for example, in transition metal-rich samples, copper, iron and steel, were eliminated by L-cystine (for As and Sn) and by LI cysteine (for Ge). The analysis of a number of standard reference materials gave excellent results of As and Sn contents in agreement with the certified values, showing there was no systematic interference. The detection limits for both germanium and tin were 20 pg ml- I . Preliminary studies were carried out for the determination of antimony and lead. Antimony was found to react with NaBH4, remaInIng from the previous determinations, giving an analytical signal. A reversed injection manner, i.e., injection of the NaBH4 solution prior to the analyte solution was used to avoid uncertainty caused by residual NaBH4 present and to ensure that an excess of NaB H4 was available. A solution of 0.4% L-cysteine was found to reduce the interference from selected transition metal ions, Co(II), Cu(II), Ni(II) and Pt(IV). Hydrochloric acid - hydrogen peroxide, nitric acid - ammonium persulphate, and potassium dichromate malic acid reaction systems for lead hydride generation were compared. The potassium dichromate - malic acid reaction medium proved to be the best with respect to reproducibility and minimal interference. Cu(II), Ni(II), and Fe(II) caused strong interference In lead determinations, which was not reduced by L-cysteine or Lcystine. Sodium citrate, ascorbic acid, dithizone, thiosemicarbazide and penicillamine reduced interferences to some extent. Further interference reduction studies were carried out uSIng a number of amino acids, glycine, alanine, valine, leucine and histidine, as possible interference reducing agents in the determination of germanium. From glycine, alanine, valine to leucine, the interference reduction effect in germanium determinations decreased. Histidine II was found to be very promising In the reduction of interference. In fact, histidine proved more efficient than L-cystine and L-cysteine In the reduction of interference from Ni(II) in the determination of germanium. Signal enhancement by easily ionized elements (EIEs), usually regarded as an interference effect in analysis by DCP-AES, was studied and successfully applied to advantage in improving the sensitivity and detection limit in the determination of As, Ge, Sn, Sb, and Pb. The effect of alkali and alkaline-earth elements on the determination of the above five hydride forming elements was studied. With the appropriate EIE, a signal enhancement of 40-115% was achieved. Linear calibration and good reproducibility were also obtained in the presence of EIEs. III

Phospha-adamantanes as ligands for palladium-catalyzed cross-coupling reactions

New and robust methodologies have been designed for palladium-catalyzed crosscoupling reactions involving·a novel·class oftertiary phosphine ligand incorporating a phospha-adamantane framework. It has been realized that bulky, electron-rich phosphines, when used as ligands for palladium, allow for cross-coupling reactions involving even the less reactive aryl halide substrates with a variety of coupling partners. In an effort to design new ligands suitable for carrying out cross-coupling transformations, the secondary phosphine, 1,3,5,7-tetramethyl-2,4,8-trioxa-6phosphaadamantane was converted into a number of tertiary phosphine derivatives. The ability of these tertiary phosphaadamantanes to act as effective ligands in the palladiumcatalyzed Suzuki cross-coupling was examined. 1,3,5,7-Tetramethyl-6-phenyl-2,4,8trioxa- 6-phosphaadamantane (PA-Ph) used in combination with Pdz(dba)3permitted the reaction of an array of aryl iodides, bromides and chlorides with a variety arylboronic acids to give biaryls in good to excellent yields. Subsequently, palladium complexes of PA-Ph were prepared and isolated in high yields as air stable palladium bisphosphine complexes. Two different kinds of crystals were isolated and upon characterization revealed two complexes, Pd(PA-Ph)z.dba and Pd(PA-Ph)zOz. Preliminary screening for their catalytic activity indicated that the former is more reactive than the latter. Pd(PAPh) z.dba was applied as the catalyst for Sonogashira cross-coupling reactions of aryl iodides and bromides and in the reactions of aryl bromides and chlorides with ketones to give a-arylated ketones at mild temperatures in high yields.

Phospha-adamantane ligands and phosphorous ionic liquids for palladium-catalyzed cross-coupling reactions /

New and robust methodologies have been designed for palladiumcatalyzed cross-coupling reactions involving a library of novel tertiary phosphine ligands incorporating a phospha-adamantane framework. The secondary phosphine, l,3,5,7-tetramethyl-2,4,8-trioxa-6-phospha-adamantane was converted into a small library of tertiary phosphine derivatives and the ability of these tertiary phosphaadamantanes to act as effective ligands in the palladium-catalyzed amination reaction and p-alkyl-Suzuki cross-coupling was examined. l,3,5,7-Tetramethyl-6- phenyl-2,4,8-trioxa-6-phosphaadamantane (PA-Ph) used in combination with Pd2(dba)3 CHCI3 facilitated the reaction of an array of aryl iodides, bromides and chlorides with a variety secondary and primary amines to give tertiary and secondary amines respectively in good to excellent yields. 8-(2,4-Dimethoxyphenyl)- l,3,5,7-tetramethyl-2,4,6-trioxa-8-phospha-tricyclo[3.3.1.1*3,7*]decane used in combination with Pd(0Ac)2 permitted the reaction of an array of alkyl iodides, and bromides with a variety aryl boronic acids and alkyl 9-BBN compounds in good to excellent yields. Subsequent to this work, the use of phosphorous based ionic liquids, specifically tetradecyltrihexylphosphonium chloride (THPC), in the Heck reaction provided good to excellent yields in the coupling of aryl iodides and bromides with a variety of olefins.

Pyruvate dehydrogenase activity in response to skeletal muscle contraction at two stimulation frequencies in pyruvate dehydrogenase kinase 2 knockout mice

Pyruvate dehydrogenase (PDH) plays an important role in regulating carbohydrate oxidation in skeletal muscle. PD H is deactivated by a set of PD H kinases (PD K 1-4) with PDK2 and 4 being the predominant isoforms in skeletal muscle. PDK2 is highly sensitive to pyruvate inhibition, and is the most abundant isoform, while PDKI and 4 protein content are normally lower. This study examined the PDK isoform content and PDHa activation in muscle at rest and 10 and 40 Hz stimulation from PDK2 knockout (PDK2KO) mice to delineate the role of PDK2 in activating the PDH complex during low and moderate intensity muscle contraction. PDHa activity was lower in PDK2KO mice during contraction while total PDK actitvity was -4 fold lower. PDK4 protein was not different, however PDKI partially compensated for the lack of PDK2 and was -56% higher than WT. PDKI is a very potent inhibitor of the PDH complex due to its phosphorylation site specificity and allosteric regulation. These results suggest that the site specificity and allosteric regulatory properties of the individual PDK isoforms are more important than total PDK activity in determining transformation of the complex and PDHa activity during acute muscle contraction.

Stereoselective synthesis of substituted hexahydro-3a,4a-diazacyclopentaphenanthren-4-ones and aminoferrocenes

This thesis explored the development of several methodologies for the stereoselective construction of ligand frameworks and some of their applications. The first segment concerns the application of an enantioselective lithiation at an Sp3_ hybridized position adjacent to nitrogen by means of the widely used and typically highly effective enantioselective lithiation with ( -)-sparteine. This investigation was intended to develop a method to install chirality into a system that would be converted into a family of diaminoylidenes for use as phosphine mimics in transition metal catalysis or as nucleophilic reagents. Molecular modeling of the system revealed some key interactions between the substrate and (-)-sparteine that provided general insight into the diamine's mode of action and should lend some predictive value to its future applications. The second portion focuses on the development of methods to access 1,2- disubstituted aminoferrocenes, an underexplored class of metallocenes possessing planar chirality. Two routes were examined involving a diastereoselective and an enantioselective pathway, where the latter method made use of the first BF3-mediated lithiation-substitution to install planar chirality. Key derivatives such as 1,2- aminophosphines, made readily accessible by the new route, were evaluated as ligands for Pd(II), Pt(II) and Ir(I). These complexes show activity in a number of transformations with both achiral and prochiral substrates. Optimization experiments were conducted to prepare enantiomerically enriched 2-substituted-I-aminoferrocenes by direct asymmetric lithiation of BF3-coordinated tertiary aminoferrocenes. A predictive computational model describing the transition state of this reaction was developed in collaboration with Professor Travis Dudding's group (Department of Chemistry, Brock University). The predicted stereochemistry of the process was confirmed by single-crystal X-ray analysis of a 2-phosphino-l-dimethylaminoferrocene derivative. Enantiomerically pure samples of the aminophosphine ligands derived from this new process have given promising preliminary results in the enantioselective hydrogenation of prochiral alkenes and warrant further stUdy in metal-mediated catalysis.

Compensatory Arm Reactions in Individuals with Parkinson’s Disease

This study examined how perturbation-evoked compensatory arm reactions in individuals with Parkinson’s disease (PD) are influenced by explicit verbal instruction. Ten individuals with PD and 15 older adults without PD responded to surface translations with or without specific instruction to reach for and grasp the handrail. Electromyographic (EMG) and kinematic recordings were taken from the reaching arm. Results showed that individuals with and without PD benefitted similarly from explicit instruction. Explicit instruction resulted in earlier (p=0.005) and larger (p<0.001) medial deltoid EMG responses in comparison to no specific instructions. Compensatory arm reactions also occurred with a higher peak medio-lateral wrist velocity (p<0.001) and higher peak shoulder abduction angular velocity (p<0.001) with explicit instruction. Explicit instruction positively influenced compensatory arm reactions in individuals with and without PD. Future research is needed to determine whether the benefits of instruction persist over time and translate to a loss of balance in real life.

Effects of Instruction on Walking and Turning Performance in Individuals with Parkinson's Disease

Parkinson’s disease (PD) is characterized by postural instability and gait impairment. Verbal instructions can reduce postural sway and improve gait performance in PD. For gait, this evidence is limited to unobstructed straight-path walking. As falls in PD often occur when turning, the purpose of this thesis was to determine if instructions can benefit turning performance in this population. Twelve individuals with PD performed two walking tasks (normal walking, walking with a 180 degree turn) under four instruction conditions (no instruction, take big steps, make larger trunk movements, focus on end and/or turn point). Task duration and trunk yaw and roll sway were calculated. In general, the results demonstrated that the instruction to take big steps improved performance for both tasks compared to providing no instruction or externally based instruction. These results suggest that instructions related to step amplitude may facilitate walking and turning performance in PD.