Mitochondria are the main site of cellular adenosine triphosphate (ATP) generation which is achieved by a series of multi-subunit complexes and electron carriers which together create the oxidative phosphorylation system (OXPHOS). Whenever a defect in any of the numerous mitochondrial pathways occurs it is commonly referred to as a mitochondrial disorder. Mitochondrial disorders are a heterogeneous group of disorders characterised by impaired energy production and include a wide range of defects of either mitochondrial DNA (mtDNA) or nuclear DNA (nDNA) encoded proteins. In cases of dysfunction in the respiratory chain (complex I to IV) it is known to be a respiratory chain deficiency (RCD) which presents a huge challenge for routine diagnosis largely due to the lack of a specific and sensitive biomarker(s). One sure way of confirming the suspicion of a RCD is by performing enzyme analysis on a muscle sample obtained through a biopsy. However, due to the lack of theatre time available to clinicians and the relative large number of false positive patients that are being selected for biopsies, it was decided to develop a biosignature to limit the number of false positive patients from the diagnostic workflow. An untargeted liquid chromatography mass spectrometry (LC-MS) metabolomics approach was used to investigate RCDs in children from South Africa. Sample preparation, a liquid chromatography time-of-flight mass spectrometry method and data processing methods were standardised. Furthermore the developed methodology made use of reverse phase chromatography in conjunction with positive electrospray ionisation (ESI) and a hydrophilic interaction chromatography (HILIC) in negative electrospray ionisation. Urine samples of 61 patients representing three different experimental groups were analysed. The three experimental groups comprised of patients with respiratory chain deficiencies, clinical referred controls (CRC) and patients suffering from various neuromuscular disorders (NMD). After a variety of data mining steps and statistical analysis a list of 12 features were compiled with the ability to distinguish between patients with RCDs and CRCs. The proposed signature was also tested on the neuromuscular disorder group, but this result indicated that the biosignature performed better when used to differentiate between patients with RCDs and CRCs, since the model was designed with this purpose. An alternative validation study is required to identify the features found with this proposed biosignature, to ensure that this biosignature can be practically implemented as a non-invasive screening method. / MSc (Chemistry), North-West University, Potchefstroom Campus, 2014

Patients that have undergone organ transplantation are life-long treated with immunosuppressant drugs and these have to be monitored regularly to get the desired effect of suppressing the immune system. To monitor the drug concentration normally a venous blood sample is collected at a clinic but the use of dried blood spots (DBS) as a matrix for drug monitoring for immunosuppressant drugs will make home sampling possible for this patient group. The aim of this study was to develop and validate a bioanalytical method for quantifying cyclosporine A and tacrolimus in dried blood spots. The method consist of punching out a 5 mm disc from a blood spot , followed by extracting the spot in a 96-well hydrophobic filter plate with 150 µL extraction solution containing internal standard (ascomycin and cyclosporine A d12) in a methanol water solution (80:20v/v%). The extract is then centrifuged through the filter plate down in a 96-deep well plate and injected on the LC-MS/MS, with an analysis time of 2.5min. The method will be validated in accordance with the guidelines set by the European Medicines Agency with additions specific to DBS. The method is not fully validated but will be in due time. The validated parameters show a robust and fast analysing method that has the prospects of being used for analysing DBS samples for patients and in the future can possibly be used by patients in home environment.

Furan wird in einer Vielzahl von Speisen durch Hitzebehandlung gebildet und ist kanzerogen in der Leber von Ratte und Maus. Durch die hohe Flüchtigkeit von Furan ist eine Expositionsabschätzung auf Basis der Kontamination von Lebensmitteln nur bedingt möglich. Ein alternativer Ansatz dazu ist die Identifizierung von Furanmetaboliten als Expositions­biomarker. Nach der Aufnahme wird Furan zunächst zum Dialdehyd cis-2-Buten-1,4-dial oxidiert. cis-2-Buten-1,4-dial besitzt mehrere elektrophile Strukturelemente, welche eine Reaktion mit Protein und DNS wahrscheinlich machen und damit zur bekannten Toxizität von Furan beitragen können. Es stellt sich in diesem Zusammenhang die Frage, ob eine Reaktion mit Protein die Reaktion mit der DNS verhindern kann und somit keine direkt gentoxischen Effekte auftreten. Für ein kanzerogenes Agens ohne direkte gentoxische Wirkung kann eine Schwellendosis unterhalb derer kein DNS-Schaden auftritt diskutiert werden. Für eine fundierte Risikobewertung bezüglich der Aufnahme von Furan über die Nahrung ist dies unabdingbar. In der vorliegenden Arbeit wurde nach der oralen Gabe von Furan im Urin von Fischer 344 Ratten nach Metaboliten gesucht. Eine Kontrollgruppe erhielt nur die Trägersubstanz Öl. Das vor und nach Exposition über jeweils zwei 24 Stunden Perioden gesammelte Urin wurde mittels einer Tandemmassenspektrometrie-Methode analysiert. Die Methode bestand aus einem Full-Scan und einer darüber gesteuerten Aufzeichnung eines Fragmentionenspektrums. Die Full-Scan-Daten wurden mit Hilfe der Hauptkomponentenanalyse untersucht. In der ersten Sammelperiode nach der Behandlung konnten durch die erste Hauptkomponente die behandelten von den unbehandelten Tieren getrennt werden. Aus den für die Trennung relevanten Verbindungen konnten fünf Biomarker strukturell aufgeklärt werden. In einer weiteren Tierstudie an Ratten und Mäusen wurde die Kinetik und die Dosis-Wirkungs-Beziehung der identifizierten Biomarker untersucht. Die gezielte LC-MS/MS-Analyse der Urine auf die identifizierten Biomarker hin zeigte, dass in der Ratte alle und in der Maus alle bis auf einen dosisabhängig anstiegen. Die Kinetik der Ausscheidung lieferte wertvolle Hinweise auf die Entstehung der Biomarker. Die Ausscheidung der Biomarker mit Lysinstruktur erfolgte über mehr als 72 Stunden. Dies war ein Hinweis auf eine Freisetzung aus Protein. Die Ausscheidung der restlichen Verbindungen erfolgte ausschließlich in den ersten 24 Stunden. Die in der Literatur vorhandenen Daten zur Gentoxizität von Furan und cis-Buten-1,4-dial sind unschlüssig und unvollständig. In der vorliegenden Arbeit wurde cis-2-Buten-1,4-dial im Ames Stamm TA104 und in L5178Y Mauslymphomzellen auf Mutagenität und Gentoxizität untersucht. Durch starke Zytotoxizität war der Konzentrationsbereich auf 4.5 µmol/Platte limitiert. Innerhalb dieses Bereich konnte mit der Vorinkubationsvariante des Ames-Tests keine Mutagenität beobachtet werden. Die L5178Y Mauslymphomzellen wurden mit Standardprotokollen für den Mikrokern-Test, Kometen-Test und den Thymidinkinase-Test untersucht. Der Konzentrationsbereich von cis-2-Buten-1,4-dial erstreckte sich bis 100 µM, konnte aber auf Grund der starken Zytotoxizität nur bis 25 µM ausgewertet werden. Dennoch konnte bereits in diesem Bereich ein 1.7- bzw. 2.2-facher Anstieg im Kometen- bzw. Thymidinkinase-Test beobachtet werden. Verglichen mit der Positivkontrolle Methylmethansulfonat hatte cis-2-Buten-1,4-dial bei einer deutlich höheren Zytotoxizität eine ähnliche Potenz bezüglich der Mutagenität und Gentoxizität. Um das DNS-vernetzende Potential von cis-2-Buten-1,4-dial zu bestimmen wurde eine Variante des Kometen-Tests verwendet. Es wurde dabei untersucht, ob die Vorbehandlung von Zellen mit cis-2-Buten-1,4-dial die durch &#947;-Strahlung induzierbaren Kometen reduzieren kann. Während die Positivkontrolle Glutaraldehyd die Kometen tatsächlich verringerte, blieb dieser Effekt bei cis-2-Buten-1,4-dial aus. Im Gegenteil, bei einer Konzentration von &#8805;100 mM konnte durch die Zunahme von Zellen mit beginnender Apoptose ein Anstieg der Kometen beobachtet werden. Obwohl cis-2-Buten-1,4-dial sehr deutliche gentoxische und mutagene Effekte zeigte, beschränkte die hohe Zytotoxizität den auswertbaren Bereich. Möglicherweise kann diese Problematik einen Teil der unschlüssigen Ergebnisse erklären, sicher ist jedoch, dass für die Untersuchung der Mechanismen der Toxizität und Kanzerogenität ein Beitrag von nicht gentoxischen Effekten diskutiert werden muss. / Furan has been found in a number of heated food items and is carcinogenic in the liver of rats and mice. Estimates of human exposure on the basis of concentrations measured in food are not reliable because of the volatility of furan. A biomarker approach was therefore indicated. Metabolism of furan includes the formation of an unsaturated dialdehyde, cis-2-butene-1,4-dial. In view of the multifunctional electrophilic reactivity of cis-2-butene-1,4-dial, adduct formation with protein and DNA may explain some of the toxic effects. DNA-adduction is a direct genotoxic effect. The major question was weather a direct genotoxicity of cis-2-butene-1,4-dial could be prevented by the reaction with protein structures. If so, the genotoxic and mutagenic effects are likely to show a threshold dose, reducing the cancer risk for low exposure levels. We searched for metabolites excreted in the urine of male Fischer 344 rats treated by oral gavage with 40 mg furan per kg body weight. A control group received the vehicle oil only. Urine collected over two 24-hour periods both before and after treatment was analyzed by a column-switching LC-MS/MS method. Data were acquired by a full scan survey scan in combination with information dependent acquisition of fragmentation spectra by the use of a linear ion trap. The full scan data was analyzed by principal component analysis (PCA). The first principal component fully separated the samples of treated rats from the controls in the first post-treatment sampling period. Five of the compounds that are responsible for the separation could be identified as the reaction product of cis-2-butene-1,4-dial with either glutathion or lysine (protein). In a second animal study rats and mice were treated with seven different doses of furan in the range from 125 µg to 8 mg per kg body weight. Dose-response and kinetic over 72 h of the seven identified biomarkers was examined by LC-MS/MS in the urine. In the rats all biomarkers showed a dose-dependent increase. In the mice one biomarker lacked of dose dependency. Different excretion profiles were attributed to the formation of either protein adducts or glutathione conjugates. Whereas the protein-derived biomarkers with a lysin moiety showed a slow excretion over more than 72 h, the glutathion-dervived biomarkers were only excreted within the first 24 h. Short-term tests for genotoxicity of furan in mammalian cells are inconclusive, little is known for cis-2-butene-1,4-dial. We investigated cis-2-butene-1,4-dial generated by hydrolysis of 2,5-diacetoxy-2,5-dihydrofuran for genotoxicity and mutagenicity in Salmonella typhimurium (Strain TA104) and in L5178Y mouse lymphoma cells. The Ames Test was negative in the preincubation assay with and without reduction of cytotoxicity by addition of glutathione after preincubation phase. Remarkable cytotoxicity limited the analysis range up to 4.5 µmol/plate. Mutagenicity and genotoxicicty in L5178Y mouse lymphoma cells was evaluated using standard procedures for the comet assay, the micronucleus test, and the mouse lymphoma thymidine kinase gene mutation assay. cis-2-butene-1,4-dial was tested at 0, 6.25, 12.5, 25, 50, and 100 µM. Cytotoxicity was remarkable; cell viability at 50 µM was reduced to <50%. Up to 25 µM, cell viability was >90%, and measures of comet assay and thymidine kinase mutations were increased over control about 1.7 an 2.2-fold, respectively. Compared to methyl methanesulfonate used as positive control, cis-2-butene-1,4-dial was of similar potency for genotoxicity but much more cytotoxic. A potential cross-linking activity of cis-2-butene-1,4-dial was investigated by checking whether gamma radiation-induced DNA migration in the comet assay could be reduced by pretreatment with cis-2-butene-1,4-dial. As opposed to the effect of the positive control glutaraldehyde, cis-2-butene-1,4-dial treatment did not reduce the comets. On the contrary, an increase was observed at &#8805;100 µM cis-2-butene-1,4-dial, which was attributable to early apoptotic cells. Although cis-2-butene-1,4-dial was found to be a relatively potent genotoxic agent in terms of the concentration necessary to double the background measures, cytotoxicity strongly limited the concentration range that produced interpretable results. This may explain some of the inconclusive results and indicates that nongenotoxic effects must be taken into account in the discussion of modes of toxic and carcinogenic action of furan.

Synthetic piperazines are chemically-produced compounds that contain a six-member ring with two opposing nitrogen atoms. Several piperazine derivatives, namely 1- benzylpiperazine (BZP), 1-(3-trifluoromethylphenyl)-piperazine (TFMPP), and 1-(3- chlorophenyl)-piperazine (mCPP), have fallen into the “designer drugs” category due to their increasing recreational use as a “legal” alternative to ecstasy (3,4-methylenedioxymethamphetamine). These compounds share similar stimulant and physiological effects with amphetamines which make them desirable to young adults in party-type atmospheres. BZP, a Schedule I drug for its high abuse potential and no accepted medical use, is the only recreationally-abused synthetic piperazine currently federally controlled in the United States. The purpose of this research was to develop and validate a reliable method to identify and quantify eight forensically significant synthetic piperazines in blood and urine using ultra-fast liquid chromatography-electrospray ionization-tandem mass spectrometry (UFLC-ESI-MS/MS). The method was validated according to the Scientific Working Group for Forensic Toxicologists (SWGTOX) guidelines for quantitative analysis for both matrices and includes the following analytes: 1-benzylpiperazine (BZP), 1-(4-fluorobenzyl)-piperazine (FBZP), 4-methyl-1-benzylpiperazine (MBZP), 1-(4-methoxyphenyl)-piperazine (MeOPP), 1-(para-fluorophenyl)-piperazine (pFPP), 1-(3-chlorophenyl)-piperazine (mCPP), 2,3-dichlorophenylpiperazine (DCPP), and 1-(3-trifluoromethylphenyl)-piperazine (TFMPP). All samples were prepared by fortifying 100 µL of certified drug-free whole blood and urine (UTAK Laboratories, Inc., Valencia, CA, U.S.A.) with certified reference standards (Cayman Chemical, Ann Arbor, MI, U.S.A.) of each analyte at desired concentrations and standard additions of 1-benzylpiperazine-d7, 1-(3-chlorophenyl)-piperazine-d8, and 1(-3-trifluoromethylphenyl)-piperazine-d4 internal standards (Cerilliant, Round Rock, TX, U.S.A). After pretreatment with 1 mL phosphate buffer, samples underwent solid phase extraction (SPE) on mixed-mode copolymeric columns (Clean Screen®, UCT Inc., Levittown, PA, U.S.A.). Eluents were evaporated to dryness with low heat (65°C) and nitrogen gas. Samples were reconstituted with a 50:50 mixture of methanol and 2mM ammonium formate buffer with 0.2% formic acid before being analyzed by a UFLC (Shimadzu Corporation, Kyoto, Japan) and 4000 QTRAP ESIMS/MS (SCIEX, Framingham, MA, U.S.A.) system. Analyses were performed with multiple reaction monitoring scans in positive ionization mode using ions and voltages obtained from a manual compound optimization. Analytes were separated on a reversed phase column (Kinetex® F5, Phenomenex®, Torrance, CA, U.S.A.) with a binary gradient consisting of a 2mM ammonium formate buffer with 0.2% formic acid and methanol with 0.1% formic acid. The flow rate was 0.400 mL/min. Analyst™ (SCIEX) software was used for data collection and MultiQuant™ (SCIEX) software was used for quantitation. The total run time was 11.5 minutes with equilibrations. All calibration curves in both matrices exhibited R2 values > 0.99 using a weighting factor of 1/x. A linear dynamic range of 20-2000 ng/mL was used for all analytes in both matrices, except for BZP in urine which ranged from 50-2000 ng/mL. In blood, the limit of quantitation was 10 ng/mL for mCPP and TFMPP and 20 ng/mL for BZP, FBZP, MBZP, MeOPP, pFPP and DCPP. In urine, the limit of quantitation was 10 ng/mL for MeOPP, mCPP, TFMPP and DCPP, 20 ng/mL for FBZP, MBZP and pFPP and 50 ng/mL for BZP. When a 200 ng/mL concentration was evaluated, the SPE procedure showed percent recoveries ranging from 80-95% for blood; except for BZP, FBZP, and MeOPP which had recoveries of 60%, 60%, and 105%, respectively. Percent recoveries ranged from 82-94% for urine; except for BZP and FBZP which had recoveries of 66% and 68%, respectively. Bias and precision were assessed at concentrations of 50, 200, and 700 ng/mL. All samples were calculated within ±20% bias and within ±20% coefficient of variation. The highest concentration evaluated that did not produce carryover in subsequent matrix blanks was 5000 ng/mL. Ionization was suppressed for all analytes in both matrices by 45-95%. Matrix effects were present but were determined to be insignificant. Of the drugs evaluated, caffeine, dibenzylpiperazine, and 1-(4-chlorophenyl)-piperazine (pCPP) produced chromatographic peaks in the method; however, pCPP was the only substance that affected quantitation of an analyte. It increased the peak area of mCPP by almost 50% when present at the same concentration which suggests this method is unable to differentiate between isomeric pairs. This is a sensitive, reliable, and robust method with a wide linear dynamic range to account for the presence of these analytes in both blood and urine. This research will provide for the identification and quantitation of these substances in forensic casework.

L’utilisation massive des antibiotiques contribue à leur accumulation dans les boues des stations d’épurations. L’application directe des boues est parmi les sources de dissémination des antibiotiques et des gènes de résistance aux antibiotiques. Le compostage et la méthanisation sont parmi les bioprocédés de traitement des boues qui permettent d’éliminer ou réduire les teneurs de certains antibiotiques. Dans ce travail, une boue primaire de la STEP de Marrakech a été contaminée par trois familles d’antibiotiques (macrolides, tétracyclines, fluoroquinolones) pour conduire 4 essais de compostage à différentes doses (dont un essai témoin) et un essai deméthanisation en mode semi-continu. Les résultats du compostage ont montré que l’augmentation des concentrations d’antibiotiques retarde la dégradation de la matière organique et affecte le ratioC/N. De même, la phase thermophile est perturbée, retardée et réduite dans le temps. Pour la méthanisation, une concentration unique et réaliste a été testée. Dans ces conditions, aucun effet sur la production du biogaz ou sur la dégradation de la matière organique n’a été observé. Afin de suivre la dissipation des trois familles d’antibiotiques utilisées au cours du compostage et de la méthanisation, une approche analytique basée sur l’extraction accélérée par solvant (ASE) suivie par l’application d’une méthode des ajouts dosés avant quantification par chromatographie liquide couplée à de la spectrométrie de masse en tandem (UPLC-MS/MS) a du être mise en point. Le compostage et la méthanisation permettent de réduire significativement les concentrations des molécules parents appartenant à la famille des macrolides et des tétracyclines. Par contre,l’élimination des fluoroquinolones est non-significative et ne dépasse pas 30%. Au cours du compostage, la dissipation des macrolides se fait en phase de stabilisation tandis que la phase de maturation est impliquée dans la dissipation des tétracyclines. Les concentrations encirprofloxacine (fluoroquinolone) semblent légèrement évoluer au cours du procédé probablement en raison d’une adsorption/désorption sur le co-substrat lignocellulosique utilisé. Concernant la méthanisation, l’élimination des macrolides et des tétracyclines est significative durant la stabilisation du procédé mais n’atteinds pas les rendements observés lors du compostage. Ladiminution des concentrations des molécules parents est probablement accompagnée par une biotransformation des antibiotiques sous forme de métabolites qui à ce stade ne sont pas connus.La question de la rémanence de certaines molécules comme les fluoroquinolones, interpelle quand au risque d’antibiorésistance. Ainsi, la valorisation des composts/digestats comme amendements organiques des sols dois à terme conduire à une réflexion concernant la réglementation qui inclus la présence de molécule de la classe des antibiotiques.

In the field of forensic toxicology, several challenges exist with quantification analysis of cocaine and metabolites in post mortem samples. Cocaine can prove difficult to detect and quantify in blood, urine, and soft tissues following extensive decomposition. Alternative matrices, such as hair, nails, and bone could prove useful in detecting chronic drug use in post-mortem toxicology cases. Detection and quantification of drugs in complex matrices is difficult to accomplish due to time-consuming extraction processes, and inability to detect an analyte at trace levels. Further, analysis of drugs in hard tissues, such as hair and bone, has only been attempted in recent years. Even fewer studies have investigated detection of drugs following decomposition of remains, specifically outdoor decomposition. The objective of this study was to develop a robust extraction and clean up methodology, in which a homogenization step precedes, to efficiently extract drugs from complex matrices, reach a target limit of detection (LOD) and to maintain instrument performance using multidimensional chromatography. Multi-dimension chromatography platform such as two dimensional liquid chromatography tandem mass spectrometry ( 2D-LC/MS/MS,) offers options not compatible with single dimension v units. With large volume injection capabilities of aqueous and organic extracts, the analytical process be reduced from multiple hours to minutes. All rat specimens used for this study fell under an Institutional Animal Care and Use Committee (IACUC) protocol. The rodents underwent a 10-12 weeks chronic intravenous self-administration of cocaine. This was followed by a six-week period of abstinence, followed again by a three-week period of cocaine self-administration before being euthanized. Average daily dosages for each rat fell within a range of 13-19 mg/kg. A total of 14 cocaine positive rats were placed outside and above ground in the Boston University Forensic Anthropology Outdoor Research Facility (Holliston, MA, U.S.A) for a period of 12 months. All recoverable skeletal samples were collected for testing. Drug free control rat bones were also acquired by placing drug-free rats outdoors, above ground, until full decomposition occurred. In this study, a method analyzing cocaine and its major metabolites benzoylecgonine and ecgonine methyl ester was developed. After homogenization of whole bones, the extraction process was performed using a mixed mode reversed-phase/ion exchange sorbent. The use of a 2D LC/MS/MS technology eliminates the need for a lengthy evaporation step in the extraction method. The chosen 2D LC/MS/MS used in this application was identified using a 6x6 automated method development protocol. The manual extraction of the bone samples was completed in less than an hour. The analysis was performed using 100μL of the final organic solvent (MeOH) extracts. vi The limit of quantitation (LOQ) for cocaine and benzoylecgonine was measured at 0.05ng/g (0.05ng/mL or 50pg/g) of sample material and the LOQ for ecgonine methyl ester was measured at 0.1ng/g (0.1 ng/mL or 100pg/g). The extraction method for cocaine proved to give a linear dynamic range of 2.5 orders of magnitude (0.05 ng/g to 10ng/g with an R2 = 0.998. The micro extraction protocol combined with a multi-dimension chromatography used in this study decreased sample preparation time without sacrificing the quality seen with current single dimension chromatography techniques. The procedure developed in this study can be utilized on bone and completed in less than an hour before injection into the 2D-LC/MS/MS system.

Antibiotics are used as prophylactic agents to promote growth and for treating infections in animals. However, the irrational use of antibiotics in livestock management is a significant cause of the development of antibioticresistant genes in the environment. Each year 2 million people suffer from the infections caused by bacteria which are resistant to antibiotics and 23,000 of these people are estimated to die because of antibiotic resistance. New drugs are continually coming into the market but are at the risk of developing resistance. Thus, there is a need for the development of analytical methods which can be used to monitor these antibiotic concentrations in environmental samples. This research is focused on developing and validating a Solid Phase Extraction (SPE) procedure and liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for quantifying tylosin antibiotic in cattle waste. Tylosin was extracted from cattle waste samples using Strata polymeric weak cation cartridges by adding a sodium-EDTA buffer solution and methanol. Chemical analysis of the extracted tylosin was performed using a Varian 212-LC HPLC and Agilent 500 Ion Trap mass spectrometric detector. The concentrations of tylosin in study group animals were compared with respect to the date of sampling and cattle body weight with a control group and results are presented.

Heart failure is a major public health issue, with its prevalence estimated to be 6.5 million adults in the USA. Of the hospitalized heart failure (HF) cases, 50% are characterized by preserved ejection function (HFpEF). In HFpEF, the heart pumps a normal proportion of blood that enters it. However, thickening of the ventricular walls inhibits the chamber filling to normal volume. The direct basis of HFpEF is a slowed elongation of the cardiac muscle during the diastolic phase of the cardiac cycle. Elucidation of mechanisms that mediate relaxation of cardiac muscle could help understand the pathogenic mechanisms in HFpEF. Myocardial contraction and relaxation are tightly controlled processes that involve thick and thin filament regulatory proteins. β-Adrenergic signaling pathway is a major regulator of myocardial contraction and relaxation via the activation of protein kinase A (PKA). Two key myofilament proteins, troponin I (TnI) and myosin binding protein-C (MyBPC), are phosphorylated by PKA following β-adrenergic stimulation. The purpose of this thesis is to develop a liquid chromatography-mass spectrometry (LC-MS) method for the quantification of phosphorylation in TnI and MyBPC and measure the changes in the degree of phosphorylation in transverse-aortic constriction (TAC) mouse hearts, a model representing HFpEF, and sham (control) mouse hearts. The initial approach of the project was to develop a method for quantification of phosphopeptides using synthesized stable isotope labeled (SIL) peptides, both with and without phosphate modification. To accomplish this goal, a multiple reactions monitoring (MRM)-LC-MS method for the quantification of the synthesized SIL peptides was first developed. This method, using low picomole amounts, is applicable to researchers in the field using SIL peptides for quantification. However, when the SIL peptides were actually applied, we determined that there was a selective absorption of some phosphate peptides in the LC column, limiting the use of the SIL peptides for quantification. This result is also of general interest to others trying to identify phosphopeptides, not realizing that some peptides will go unmeasured. Thus, we returned to expanding an earlier method developed in our research group to quantify the degree of phosphorylation. Key to this work was the development of a quantification method directly from heart myofibrillar protein preparations without requiring isolation of individual proteins by gel electrophoresis. Using the LC-MS method developed, we quantified phosphorylation sites of TnI and MyBPC in the TAC and control mouse hearts. The phosphorylation measurements showed no significant difference in phosphorylation between the TAC and control mice, except for one site, S302 in MyBPC that had a 13% decrease in phosphorylation with TAC. We conclude that in our TAC model, PKA dysfunction may not play a role in the initial development of HFpEF.

Nicotinamide adenine dinucleotide (NAD+) is a cofactor in hydride transfer reactions and consumed substrate of several classes of glycohydrolyitc enzymes, including sirtuins. NAD+, its biosynthetic intermediates, breakdown products, and related nucleotides (the NAD metabolome) is altered in many metabolic disorders, such as aging and obesity. Supplementation with the novel NAD+ precursor, nicotinamide riboside (NR), ameliorates these alterations and opposes systemic metabolic dysfunctions in rodent models. Based on the hypothesis that perturbations of the NAD metabolome are both a symptom and cause of metabolic disease, accurate assessment of the abundance of these metabolites is expected to provide insight into the biology of diseases and the mechanism of action of NR in promoting metabolic health. Current quantitative methods, such as HPLC, lack specificity and sensitivity to detect distinct alterations to the NAD metabolome. In this thesis, I developed novel sensitive, accurate, robust liquid chromatography mass spectrometry methodologies to quantify the NAD metabolome and applied these methods to determine the effects of disease states and NR supplementation on NAD+ metabolism. My investigations indicate that NR robustly increases the NAD metabolome, especially NAD+ in a manner kinetically different than any other NAD+ precursor. I provide the first evidence of effective NAD+ supplementation from NR in a healthy, 52 year old human male, suggesting the metabolic promoting qualities of NR uncovered in rodent studies are translatable to humans. During my investigation of NR supplementation, my work establishes an unexpected robust, dramatic increase in deamino–NAD+, NAAD, directly from NR, which I argue could serve as an accessible biomarker for efficacious NAD+ supplementation and the effect of disease upon the NAD metabolome. Lastly, I further establish NR as a general therapeutic against metabolic disorder by detailing its ability to oppose aspects of chronic alcoholism and diabetes mellitus.

The purpose of the studies included in this thesis is to develop an effective an efficient method to study the proteome using separation and detection of peptides, when only a limited amount of sample, 10 micrograms of total protein or less, is available. The analysis will be applied to multiple myeloma cancer cells using ultra high-performance liquid chromatography-mass spectrometry for expression proteomics to illustrate utility. To detect low abundance peptides in a complex proteome, we use different strategies, including basic pH reversed-phase liquid chromatography (bRPLC), mass-to-charge fractionation in the mass spectrometer, and various liquid chromatography gradients to increase peptide separation to improve opportunities for detection and quantification. The different methods are optimized and compared by the number of peptides detected. Step-wise elution of bRP spin columns proved to yield more than 36,000 peptides using only 10 μg of protein. Mass-to-charge (m/z) fractionation was tested in mass analyzer Q-Exactive Plus (Thermo Scientific). Liquid chromatography-tandem mass spectrometry (LC-MS/MS) of an unfractionated sample was analyzed 4 times at different mass ranges, each mass range width of 150 m/z, resulting from 4 spectra combined, 31,732 peptides representing 3,967 proteins. Showingcomparable results to those form high pH reversed phase fractionation spin columns 5 fractions. Establishing a benchmark where the LC-MS/MS analysis of 600 μg of 10plex TMT-labeled peptides fractionated with bRPLC into 24 fractions yielded over 74,000 peptides from 7,700 proteins, we compared those results with analysis of 10 μg of total TMT-labeled peptides fractionated by bRP spin columns into 5 fractions, which produced 14,019 peptides from 3,538 proteins. These experiments were used to relatively quantify protein expression in naïve and drug resistant multiple myeloma cells lines as an example application in cancer research.