Browsing by Subject "HPLC"
Now showing items 1-13 of 13
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(2019)The rapid emergence of drug resistant pathogens prevents effective treatment of diseases and threatens the lives of millions of people. Similarly, resistance to chemotherapeutic agents has been observed in several types of cancer. Therefore, screening for novel antimicrobial and antileukemic substances is urgently needed. Screening microorganisms for bioactive molecules has resulted in the discovery of several substances that are currently used for disease treatment. Cyanobacteria represent an ancient group of oxygenic, photosynthetic prokaryotes that produce a variety of functionally diverse and structurally complex natural compounds, some of which have already been used as source of inspiration in drug development process. In this study, I evaluated the antimicrobial and antileukemic potential of filamentous cyanobacteria against Gram-positive, Gram-negative and fungal potential pathogens and acute myeloid leukemia (AML) MOLM-13 cell line. Extracts showing antibiotic and/or antileukemic activity were subjected to reversed-phase HPLC and individual fractions were re-evaluated for their ability to kill the abovementioned pathogens and/or induce cell death in MOLM-13 cell line. Metabolites present in the active HPLC fractions were analysed by UPLC/ESI/Q-TOF and elemental compositions were obtained. Identification of metabolites was accomplished by searching online databases for compounds with identical elemental composition. Chemical structures were further confirmed by comparing mass spectrometry data with publicly available data. New bioactive metabolites, new variants of known metabolites and a number of yet unidentified metabolites exhibiting antimicrobial and/or antileukemic activity are reported herein. In detail, novel metabolites belonging to aromatic polyketides and their new variants were present in the active fractions of Nostoc sp. CENA69. The cyanobacterium Aliinostoc sp. CENA513 produced the recently discovered metabolite nocuolin A, a compound with antimicrobial and antiproliferative properties, lipids and unidentified lipidic compounds that showed only bactericidal activity against B. cereus. Interestingly, none of the abovementioned strains had any effect on the growth of Gram-negative pathogens. Planktothrix agardhii UHCC 0018 and Anabaena sp. UHCC 0187 strains showed only antileukemic activity. The majority of the bioactive fractions deriving from these two strains contained either lipids or pigments and their derivatives. The remaining active HPLC fractions of these two strains contained a great number of unidentified compounds. Further studies are required to identify the unknown compounds and purify the novel metabolites and antibacterial lipids. The results presented herein clearly show that Cyanobacteria are an emerging source of bioactive metabolites that can be used in drug development process or act as a source of inspiration for the production of novel synthetic drugs.
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(2019)The rapid emergence of drug resistant pathogens prevents effective treatment of diseases and threatens the lives of millions of people. Similarly, resistance to chemotherapeutic agents has been observed in several types of cancer. Therefore, screening for novel antimicrobial and antileukemic substances is urgently needed. Screening microorganisms for bioactive molecules has resulted in the discovery of several substances that are currently used for disease treatment. Cyanobacteria represent an ancient group of oxygenic, photosynthetic prokaryotes that produce a variety of functionally diverse and structurally complex natural compounds, some of which have already been used as source of inspiration in drug development process. In this study, I evaluated the antimicrobial and antileukemic potential of filamentous cyanobacteria against Gram-positive, Gram-negative and fungal potential pathogens and acute myeloid leukemia (AML) MOLM-13 cell line. Extracts showing antibiotic and/or antileukemic activity were subjected to reversed-phase HPLC and individual fractions were re-evaluated for their ability to kill the abovementioned pathogens and/or induce cell death in MOLM-13 cell line. Metabolites present in the active HPLC fractions were analysed by UPLC/ESI/Q-TOF and elemental compositions were obtained. Identification of metabolites was accomplished by searching online databases for compounds with identical elemental composition. Chemical structures were further confirmed by comparing mass spectrometry data with publicly available data. New bioactive metabolites, new variants of known metabolites and a number of yet unidentified metabolites exhibiting antimicrobial and/or antileukemic activity are reported herein. In detail, novel metabolites belonging to aromatic polyketides and their new variants were present in the active fractions of Nostoc sp. CENA69. The cyanobacterium Aliinostoc sp. CENA513 produced the recently discovered metabolite nocuolin A, a compound with antimicrobial and antiproliferative properties, lipids and unidentified lipidic compounds that showed only bactericidal activity against B. cereus. Interestingly, none of the abovementioned strains had any effect on the growth of Gram-negative pathogens. Planktothrix agardhii UHCC 0018 and Anabaena sp. UHCC 0187 strains showed only antileukemic activity. The majority of the bioactive fractions deriving from these two strains contained either lipids or pigments and their derivatives. The remaining active HPLC fractions of these two strains contained a great number of unidentified compounds. Further studies are required to identify the unknown compounds and purify the novel metabolites and antibacterial lipids. The results presented herein clearly show that Cyanobacteria are an emerging source of bioactive metabolites that can be used in drug development process or act as a source of inspiration for the production of novel synthetic drugs.
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(2010)The literature review elucidates the mechanism of oxidation in proteins and amino acids and gives an overview of the detection and analysis of protein oxidation products as well as information about ?-lactoglobulin and studies carried out on modifications of this protein under certain conditions. The experimental research included the fractionation of the tryptic peptides of ?-lactoglobulin using preparative-HPLC-MS and monitoring the oxidation process of these peptides via reverse phase-HPLC-UV. Peptides chosen to be oxidized were selected with respect to their amino acid content which were susceptible to oxidation and fractionated according to their m/z values. These peptides were: IPAVFK (m/z 674), ALPMHIR (m/z 838), LIVTQTMK (m/z 934) and VLVLDTDYK (m/z 1066). Even though it was not possible to solely isolate the target peptides due to co-elution of various fractions, the percentages of target peptides in the samples were satisfactory to carry out the oxidation procedure. IPAVFK and VLVLDTDYK fractions were found to yield the oxidation products reviewed in literature, however, unoxidized peptides were still present in high amounts after 21 days of oxidation. The UV data at 260 and 280 nm enabled to monitor both the main peptides and the oxidation products due to the absorbance of aromatic side-chains these peptides possess. ALPMHIR and LIVTQTMK fractions were oxidatively consumed rapidly and oxidation products of these peptides were observed even on day 0. High rates of depletion of these peptides were acredited to the presence of His (H) and sulfur-containing side-chains of Met (M). In conclusion, selected peptides hold the potential to be utilized as marker peptides in ?-lactoglobulin oxidation.
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(2021)The literature study of this thesis focuses on the different analytical methods used to analyse amino acids in food and beverage samples. Amino acids are essential organic molecules and their concentrations in foods and beverages constitute, inter alia, the product’s nutritional value, quality, freshness, and flavour. Amino acid analysis of foodstuff has various applications, which exploit several analytical methods. These reviewed methods are founded on academic articles published during the past two decades. This literature review discusses the different sample matrixes, sample preparation methods, ways to derivate analytes, and different separation and detection methods utilized in the recent amino acid studies. The experimental part of this thesis was a modification of L-asparagine and L-aspartic acid test (L-Asp/L-AspAc) in Thermo Fisher Scientific Oy industrial R&D laboratory. An enzymatic photometric method is used to determine L-Asp/L-AspAc amino acids in food samples. The modification process entailed pre-testing of several candidate methods, from which the most suitable one was selected. The feasibility of the chosen test was affirmed before verification and validation of the modified test.
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(2013)Rhazya stricta Decne. is a small evergreen shrub belonging to the Apocynaceae family. The plant grows in South Asia and the Middle East, and in these areas it is used in traditional medicine. All parts of the plant are used in different preparations for a variety of purposes such as infections, bowel diseases, itching and diabetes. R. stricta synthesizes about a hundred different alkaloids, of which only a fraction has been studied closer. Some of the analyzed alkaloids have showed some interesting pharmacological properties such as antibacterial and cytotoxic properties. Because it is often both economically and ecologically unsustainable to cultivate or to collect large amounts of medicinal plants from nature, cell cultures have been developed from plants. The properties and synthesized substances of the cell cultures can be analysed and modified in laboratories. In the experimental part of this work, a system was developed for alkaloid extraction, fractionation and isolation from dried cell material from cultured R. stricta hairy root-cells. The goal was to develop a functioning system that eventually enables identification of the alkaloids synthesized by the cultured cells under given conditions. Alkaloids were extracted from 26 g of dried and ground cell mass. The fractionation of the alkaloids was performed with medium pressure liquid chromatography (MPLC) and the fractions were analyzed by thin-layer chromatography (TLC) and high-performance liquid chromatography (HPLC). The alkaloids were purified by horizontal TLC and preparative HPLC. Ion-pair chromatography was used for analyzing the extract, fractions and purified alkaloids. Five components from two fractions were eventually isolated. One of the components was tentatively identified as vincanine, but further analyzes have to be performed to identify all components reliably. In total, hairy root-cells seem to synthesize approximately 20 alkaloids with variable polarity.
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(2012)Estradiol is a female sex hormone which is metabolized to two different catechol estradiols. 2-hydroxyestradiol (2-OHE2) is normally the major catechol estradiol metabolite but breast cancer patients have increased amounts of genotoxic 4-hydroxyestradiol (4-OHE2) and it arises to predominant metabolite with these patients. These catechol estradiols can form reactive quinones that can bind to DNA and lead to mutations and finally cause cancer. Catechol-O-methyl transferase can add methyl groups and UDP-glucuronosyl transferase (UGT) glucuronic acid groups to catechol estradiols. These phase II enzymes play important role in the inactivation of catechol estradiols because only non-conjugated catechol estradiols can be oxidized to quinones. The aim of this study was to find out which human UGTs catalyze glucuronidation of 2-OHE2 or 4-OHE2, how many different glucuronides are formed and in which part of the substrate glucuronic acid is added. To answer these questions chromatography methods for 2-OHE2 and 4-OHE2 glucuronides were developed using HPLC. Eleven UGT-enzymes glucuronidate 2-OHE2. UGTs 1A1, 1A7 and 1A10 form two different glucuronides and UGTs 1A3, 1A8, 1A9, 2A1, 2A2, 2A3, 2B7 and 2B15 form only the second glucuronide. It was possible to detect three different glucuronides for 4-OHE2 but the amount of the first glucuronide was under quantification limit. UGT1A10 catalyzed the formation of the second glucuronide and UGTs 1A7, 1A8, 1A9, 2B7 and 2B15 catalyzed the formation of the last glucuronide. One aim of the study was to find out which part of the substrate is glucuronidated but this aim was not achieved because suitable standards were not available.
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(2021)Plant cell culture can be used for the production of valuable secondary metabolites. Inspired by the previous studies focusing on capsaicinoid production, this study aimed for establishing plant cell cultures of Capsicum chinense to produce capsinoids. Capsinoids are non-pungent capsaicinoid analogues with potential health benefits. Another aim of this study was to determine the α-solanine content in Capsicum plants and cell cultures to ensure that no toxic amounts are formed during the cell culture. Cell cultures of non-pungent Capsicum chinense cultivars, Trinidad Pimento and Aji Dulce strain 2, were established, and the cultures were fed with intermediates, vanillin and vanillyl alcohol, to enhance the production. In addition, cell cultures of extremely pungent Trinidad Scorpion cultivar were established and they were fed with vanillyl alcohol to study if this would result in formation of capsinoids instead of capsaicinoids. A high-performance liquid chromatography (HPLC) method with UV detection was validated for determining the capsiate contents of the cell culture samples and fruit samples for comparison. To analyze the α-solanine content of the cell culture samples and leaves and flowers of three cultivars belonging to three different Capsicum species, an HPLC-UV method was validated for this purpose as well. Despite validating a sensitive and specific method for capsiate analysis, no detectable amounts of capsiate were detected in any of the cell culture samples. Cell cultures of pungent cultivars did not produce detectable amounts of capsaicinoids either. Results from analyzing the real fruit samples were in accordance with previous literature reports, and Aji Dulce fruits were found to contain higher amounts of capsiate compared to Trinidad Pimento, although having only one indoor grown Aji Dulce fruit analyzed limits the reliability. The analytical method for determining α-solanine content had problems with internal standard and specificity. This method could be used for making rough estimates about the possible α-solanine content. No hazardous amounts were detected in any of the cell culture samples. Only one sample consisting of Aji Dulce young leaves could contain α-solanine slightly above the limits set for commercial potatoes. Results with flowers of Rocoto San Pedro Orange (C. pubescens) and Aji Omnicolor (C. baccatum) were inconclusive and it couldn’t be ruled out that they might contain large amounts of α-solanine. The reason why capsinoids, or even capsaicinoids, were not detected in the cell culture samples remains unsolved, but it could be speculated that capsinoids might degrade in the cell culture environment or that selection of cultivar or cell line is critical. This study gave further proof to the previous assumptions that chili leaves are safe and should not contain notable amounts of α-solanine.
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(2021)Plant cell culture can be used for the production of valuable secondary metabolites. Inspired by the previous studies focusing on capsaicinoid production, this study aimed for establishing plant cell cultures of Capsicum chinense to produce capsinoids. Capsinoids are non-pungent capsaicinoid analogues with potential health benefits. Another aim of this study was to determine the α-solanine content in Capsicum plants and cell cultures to ensure that no toxic amounts are formed during the cell culture. Cell cultures of non-pungent Capsicum chinense cultivars, Trinidad Pimento and Aji Dulce strain 2, were established, and the cultures were fed with intermediates, vanillin and vanillyl alcohol, to enhance the production. In addition, cell cultures of extremely pungent Trinidad Scorpion cultivar were established and they were fed with vanillyl alcohol to study if this would result in formation of capsinoids instead of capsaicinoids. A high-performance liquid chromatography (HPLC) method with UV detection was validated for determining the capsiate contents of the cell culture samples and fruit samples for comparison. To analyze the α-solanine content of the cell culture samples and leaves and flowers of three cultivars belonging to three different Capsicum species, an HPLC-UV method was validated for this purpose as well. Despite validating a sensitive and specific method for capsiate analysis, no detectable amounts of capsiate were detected in any of the cell culture samples. Cell cultures of pungent cultivars did not produce detectable amounts of capsaicinoids either. Results from analyzing the real fruit samples were in accordance with previous literature reports, and Aji Dulce fruits were found to contain higher amounts of capsiate compared to Trinidad Pimento, although having only one indoor grown Aji Dulce fruit analyzed limits the reliability. The analytical method for determining α-solanine content had problems with internal standard and specificity. This method could be used for making rough estimates about the possible α-solanine content. No hazardous amounts were detected in any of the cell culture samples. Only one sample consisting of Aji Dulce young leaves could contain α-solanine slightly above the limits set for commercial potatoes. Results with flowers of Rocoto San Pedro Orange (C. pubescens) and Aji Omnicolor (C. baccatum) were inconclusive and it couldn’t be ruled out that they might contain large amounts of α-solanine. The reason why capsinoids, or even capsaicinoids, were not detected in the cell culture samples remains unsolved, but it could be speculated that capsinoids might degrade in the cell culture environment or that selection of cultivar or cell line is critical. This study gave further proof to the previous assumptions that chili leaves are safe and should not contain notable amounts of α-solanine.
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(2016)Prolyl oligopeptidase (PREP) is a serine protease which is extensively present in the mammalian system and especially abundant in the brain. Despite the long research history of PREP its physiological function has remained unclear. PREP has been suggested to regulate the functions of many bioactive peptides by hydrolysis and on the other hand to participate in several intracellular processes probably via direct protein-protein interactions. One of the functions suggested for PREP is the regulation of the brain neurotransmitter systems and based on, for instance, the location in the brain PREP has been connected to both excitatory and inhibitory neurotransmitter systems. The literature review of this thesis first describe the brain neurotransmitter systems associated to PREP in general with some examples of diseases related to their malfunctions. In addition the structure of PREP and its location in the brain, both subcellular and cellular levels, and in distinct neurotransmitter systems, are presented, after which the different proposed functions for PREP are reviewed. The aim of the experimental part of this thesis was to investigate the effects of PREP on the brain neurotransmitter concentrations in the mouse nigrostriatal pathway and also to mouse motor behavior. The main research methods were microdialysis, tissue assays and cylinder test. The study was composed of two sections with five week duration each. The first section was performed with wild-type mice expressing naturally PREP and the second section with PREP-knockout (ko) mice and their wild-type littermates. The mice were injected unilaterally above the substantia nigra with adeno associated (AAV1) hPREP viral vector or with AAV1-eGFP (green fluorescent protein) viral vector as a control treatment. The cylinder test was carried out before the injection, and two and four weeks afterwards. Microdialysis was used to study the actions of PREP on the extracellular concentrations of dopamine (DA) and its metabolites dihydroxyphenylacetic acid (DOPAC) and homovanillic acid (HVA), gamma-aminobutyric acid (GABA) and 5-hydroxyindoleacetic acid (5-HIAA), the major metabolite of serotonin (5-HT). In addition to the baseline assay the concentrations were measured after two amphetamine treatments (10 and 30 µM) administered via the microdialysis probe. The probe guide cannulas were inserted to mice striatums 1-2 weeks before the microdialysis measurement. In the end of the experiment the tissue concentrations of DA, DOPAC, HVA, 5-HT and 5-HIAA were measured from striatum and substantia nigra. Both the microdialysis and tissue sample concentrations were quantified with high performance liquid chromatography. In the first study section the PREP enzyme activity was also determined from striatum. Neither the complete deprivation nor over-expression of PREP in the nigrostriatal pathway had clear or consistent effects on the levels of neurotransmitters studied when compared to naturally occurring PREP expression. When comparing the differences between control treated groups of PREP-ko and littermate mice, a greater amphetamine stimulated DA-levels was seen in the former group proposing negative regulatory influence of PREP. In both study sections the tissue assay results were difficult to interpret due to observed responses also with AAV1-eGFP control treatment in comparison with untreated side of the brain. This was seen as a lower DA- and DOPAC-levels in substantia nigra and thus the meaning of the changes caused by PREP treatment is hard to comprehend. The results of the cylinder test may implicate some protective effect of the PREP-ko-genotype against viral vector injections in general. Then again the existence of compensatory mechanisms is possible when using knockout animals and thus the genotype differences are hardly ever unequivocal. The results of this thesis do not suggest outright regulatory effects of PREP on the neurotransmitter functions in the mouse nigrostriatal pathway although the confirmation of this requires further studies, especially in regard to GABAergic and glutamatergic systems. Studies should include a scale of different behavioral tests of motor activity and repeated microdialysis experiment with some defining method changes. The possible function and mechanisms of PREP as a regulator of neurotransmitter intake or release is rationale to study at molecular level with applicable methods.
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(2014)Divicine and isouramil are the causative agents of favism. The stability of divicine is of vital importance in faba bean detoxification. The literature review of this thesis focused on the hydrolysis of vicine to divicine, the oxidation processes of divicine and its stability studies. The main aims of this thesis were to produce divicine using the hydrolysis of vicine with ?-glucosidase, and study the effects of nitrogen/air atmosphere, reducing agent, pH and temperature on the stability of divicine. The identities of other compounds observed in vicine hydrolysis were also to be investigated. In addition, convicine was also hydrolyzed in the extracts and pure convicine fractions. Vicine and convicine were co-extracted from dehulled faba bean flour and were separated with preparative HPLC-MS. The extracts and the pure vicine and convicine fractions were hydrolyzed with ?-glucosidase to yield divicine and isouramil. The identities of the compounds formed during vicine fraction hydrolysis were studied by MS. In the following stability studies, the pure vicine fractions were hydrolyzed with ?-glucosidase under nitrogen and in the presence of (+)-sodium L-ascorbate. Moreover, the fractions were firstly hydrolyzed under air, next, the formed divicine was incubated at pH 3.0 or 5.0 at 20 or 37 ºC. An analytical HPLC method was used to study the changes during hydrolysis and stability tests. It was found that higher ?-glucosidase concentration and longer incubation period resulted in higher hydrolysis degrees of vicine and convicine. Further, vicine was hydrolyzed more rapidly at pH 3.0 than 5.0. Vicine was hydrolyzed to divicine. Divicine further generated two compounds, named compound 1 and compound 2 in this thesis. Their corresponding retention times and absorption maxima were: 2.15 min, 282 nm; 1.79 min, 262 nm; and 1.94 min, 210 nm. Compound 1 was directly generated from divicine. It was possibly oxidized divicine, but its characterization with MS failed in this study. Compound 1 decomposed to compound 2 at pH 5.0 at 20 ºC, but at pH 3.0 at 20 ºC, divicine might directly decompose to compound 2. Only one compound (named compound 3) was formed during convicine hydrolysis, and its retention time and absorption maximum were 2.50 min and 280 nm. Divicine and compounds 1, 2, and 3 were not stable, they finally decomposed to non-UV absorbing substances. Divicine was more stable under nitrogen than under air, and in the presence of (+)-sodium L-ascorbate than without its presence. Divicine decomposed similarly at pH 3.0 and 5.0 at 37 ºC, but at 20 ºC, divicine was more stable at pH 5.0. At both pH values, the stability of divicine was increased at 20 ºC compared with 37 ºC.
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(2022)The literature section of this thesis provides an overview of modern ion-mobility spectrometry techniques in context with recent applications in analytical chemistry. While ion-mobility spectrometry is an “old” separation technique, it has received in recent years increasing attention for its unique ability to achieve separation of isomeric molecular species. Ion-mobility spectrometry can be readily hyphenated with chromatographic and mass spectrometric techniques, introducing an additional separation dimension with the unique capability of differentiating isobaric analyte ions based on their collision cross sections. After a brief introduction into the theory of ion-mobility spectrometry, most recent applications in the field are presented with the focus being on the discrimination of small isomeric molecules. The research project section of the thesis reports the synthesis of isomerically pure standard materials of the commercially unavailable pepper alkaloids piperettine and piperettyline, and the qualitative and quantitative analysis of piperettine in selected pepper fruit samples. Strategies for the synthesis of piperettine reported in the literature are reviewed, and critically evaluated in terms of practicability and overall yields. A new, expedient, and operationally convenient synthetic approach to isomerically pure piperettine and piperettyline from inexpensive starting materials is described. In course of stability studies, both alkaloids were found to be stable in the crystalline states and as solutions in a range of organic solvents under exclusion of ambient light. However, diluted solutions of both compounds proved extremely photosensitive, with extensive double bond isomerization occurring within seconds upon sunlight exposure. An analytical method for the quantification of piperettine in pepper fruit samples was developed, involving liquid extraction, extract clean-up by solid-phase extraction, and HPLC-UV analysis. The use of a chiral stationary phase (Chiralpak IB) under optimized reversed phase condition allowed for the first time clean separation of piperettine from its naturally co-occurring isomers, and thus for its unambiguous quantification. Subsequently, this method was employed to quantify piperettine in black, green, white, and red long pepper samples. The observed piperettine content were 1.4 – 3.7 mg/g in the pepper fruit samples, representing 46 – 69% of the total sum of isomers.
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(2014)Parkinson's disease causes changes in the basal ganglia GABAergic neurotransmission in addition to the well-known dopaminergic changes. These GABAergic modulations may cause somed of the symptoms not responding well to the standard dopaminergic medication. Neurotrophic factors are a group of endogenous proteins showing promise as a future treatment for Parkinson's disease. They are known to have neuroprotective and neurorestorative effects on the dopaminergic cells. Their effects to the GABAergic cells are still mostly unknown. Intrastriatal injection of GDNF to rats caused significantly slower weight gain compared to CDNF, MANF one week after stereotaxic operation (p=0,002 for CDNF vs. GDNF and p<0,001 for MANF vs. GDNF). Difference to the vehicle (phosphate buffered saline) used as a negative control was not statistically significant (p=0,055). Three weeks after the operation the differences between the treatment groups were no longer statistically significant. Because of problems with the separation in analysis, microdialysis samples remain still to be analysed. To help the analysis of GABA in the future we determined the analytical parameters of the analytical apparatus. We also defined differences in probe permeability between 1 mm and 2 mm probes and between old and new batches. GABA analysis was performed with a HPLC-fluorometric detection of o-phtaldialdehyde-derived GABA. Detection limit for old apparatus was 7,2 nM and for new apparatus 6,2 nM in a sample of 15 µl (0,11 pmol and 93 fmol respectively). Quantification limits defined were 22 nM and 19 nM (0,33 pmol and 0,28 pmol) for the old and the new apparatus, respectively. Upper limit of quantification was estimated to be 246 nM (3,7 pmol). Probes had significant differences in permeability between 1 mm and 2 mm probes, as well as between batches. The variance of permeability of 1 mm probes was estimated to be approximately twofold compared to the 2 mm probes. Furthermore the permeability of 1 mm probes varied between batches significantly. An average of permeability of the old batch was 34 % lower than that of a new batch (p<0,001).
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(2020)Ribonukleiinihapot (RNA) toimivat kriittisissä biologisissa tehtävissä geneettisen tiedon välittäjinä solun sisällä. Sen lisäksi niillä on merkittävä rooli perintöaineksen säilymisessä ja siirtymisessä sekä katalyyttisten toimintojen ylläpitämisessä. RNA-modifikaatioiden on katsottu toimivan ylimääräisenä tiedonvälittäjäkerroksena solufysiologian säätelemisessä nukleotidisekvenssien koodauksessa. Tämän Pro gradun kirjallisuusosassa esitellään viimeisten viiden vuoden ajalta (2014-2019) vakiintuneet tekniikat sekä ohjelmistot RNA-modifikaatioiden tutkimuksissa. RNA-modifikaatioiden monimuotoisten biologisten toimintojen selvittäminen perustuu tarkkaan detektointiin, kvantitointiin, ja modifikaatioiden kartoitukseen. Näytteen esikäsittely mm. kemiallinen leimaaminen on tärkeässä roolissa onnistuneen analyysin kannalta. Työssä kerrotaan mm. massaspektrometrisistä (MS) identifioinneista ja rakennetutkimuksista sekä sekvenssointtitekniikoiden hyödyntämisestä. Useiden viime vuosien aikana menetelmien kehittämisessä on edistytty merkittävästi. Erityisesti MS datan käsittelyyn soveltuvia ohjelmistoja on luotu tandemmassaspektrien tulkitsemiseksi. Massaspektrien käsittelyn monipuolistaminen on johtanut uusiin lähestymistapoihin. joista voidaan saada kvalitatiivista ja kvantitatiivista tietoa RNA-modifikaatioista, usein jopa sekvenssispesifisyyden tasolla. Koska RNA-tutkimus on vielä varhaisessa vaiheessa, se vaatii paljon tutkimustyötä. Uusien menetelmien, tekniikoiden ja ohjelmistojen kehittymisen myötä ymmärrys RNA-modifikaatioiden olemassaolosta, tarkoituksesta, toiminnasta ja vaikutuksesta elämään kasvaa. Työn kokeellisen osion aiheena oli derivatisoida lähettiribonukleiinihappo (mRNA) fluorisoivaksi ja kehittää analyyttinen erotusmenetelmä kapillaarielektroforeesilla (CE) laserindusoitua fluoresenssidetektoria (LIF) käyttäen. Fluoreskeiini-5-isotiosyanaatti (FITC) valittiin derivatisointireagenssiksi sen monipuolisen käytettävyyden vuoksi ja helpon saatavuuden takia. Edellisestä huolimatta on yleisesti tiedossa FITC:n nopea hajoaminen, mutta tähän asti ei ole raportoitu, kuinka nopeasti FITC todellisuudessa muuttuu reagointikyvyttömäksi. Menetelmän kehitysvaiheessa käytettiin RNA-tyyppisiä biologisia molekyylejä, kuten BSA ja aminohappoja. Työssä testattiin erilaisia puskureita eri pH-arvoilla ja pitoisuuksilla. Lisäksi optimoitiin injektiopaine ja -aika sekä virta käyttäen CE-laitteistoa varustettuna diodirividetektorilla (CE-UV). Koska työn päätavoitteena oli erotusmenetelmän kehittäminen, derivatisointireaktion toimivuuteen ei heti kiinnitetty tarpeeksi huomiota. Menetelmä optimoitiin leimatuille aminohapoille ja BSA:lle. Lopuksi siirryttiin viimeistelemään menetelmä CE-LIF:llä. Derivatisointituotteiden tunnistus tehtiin ESI-TOF-MS:lla. Siinä yhteydessä huomattiin FITC:n nopea hajoaminen. Monien haasteellisten kokeilujen jälkeen päädyttiin keskittyä FITC:n stabiiliuden selvittämiseen. FITC:ä myydään samalla cas-numerolla kahta eri konformeeria ja tämän lisäksi vielä eri cas-numerolla kahta isomeeria. Näillä kaikilla on hieman erilaiset fysikaaliset ominaisuudet, jotka selvitettiin tässä työssä. Tutkittiin FITC:n eri konformeerien stabiilisuutta erilaisissa liuottimissa ja kahdessa lämpötilassa kymmenen päivän ajan käyttäen ESI-TOF-MS-laitetta sekä positiivisella että negatiivisella polariteetilla. Tutkimuksessa standardoidulla derivatisointiproseduurilla testattiin FITC-kemikaalin avulla LIF-detektorin toimintaa. Kuitenkin mRNA-derivatisointiin vaaditaan kalliit leimauskitit, joita ei tässä vaiheessa ollut mahdollista hankkia. Pysyminen alkuperäisessä suunnitelmassa ja optimoida CE-LIF -metodi fluoresoivalla FITC-reagenssilla lähetti-RNA:n leimaamiseen ei aikataulullisesti onnistunut. Siten projekti painottui tämän kokeellisen työn osalta derivatisoinnin optimointiin ja FITC-kemikaalien kinetiikkaan. Sen vuoksi projektissa tehtiin perusteellinen pohjatyö tuleville tutkimuksille. Kokeellisesti onnistuttiin leimaamaan nukleotidiemäksiä, jotka ovat lähetti-RNA:n perusosia. Selvitettiin FITC:n hajoamisnopeus ja liuottimet, joita FITC-tutkimuksissa on käytetty ja joita tulee käyttää, jotta reaktio onnistuu. Leimaus onnistui p-kinoidille. Saatujen tulosten perusteella on mahdollista laskea FITC:n optimaalinen määrä onnistuneen reaktion kannalta. Lisäksi osoitettiin, että leimausreaktio on herkkä, kun käytetään optimaalista puskuria ja optimipitoisuuksia. Jatkotutkimuksissa myös FITC-liuoksen valmistamiseen pitää kiinnittää paljon huomiota.
Now showing items 1-13 of 13