Dissertations / Theses on the topic 'Medical Biochemistry and Clinical Chemistry'

Molecular biomarkers are chemical signatures that all cell types possess. They are used in medicine to evaluate both normal biological events and pathogenic processes. A series of biomarkers associated with cancer of the breast, ovaries and other parts of the female reproductive tract and the monitoring of pregnancy were measured in disease‐free women. The biomarkers measured were prostate specific antigen (PSA), CA125, CA15‐3, CA72‐4, and pregnancy associated plasma protein‐a (PAPP‐A). The patterns of change during natural and stimulated ovarian cycles and early pregnancy were investigated to determine if these biomarkers could reflect normal events relating to ovulation and implantation/placentation. In addition, the study was able to investigate the possible erroneous crossing of clinical cut‐off values associated with disease due to other biological processes rather than the disease itself. total of 73 blood samples (10 women) taken throughout the natural menstrual cycle, 64 blood samples (11 women) during stimulated ovarian cycles and 86 blood samples (14 women) during early pregnancy monitoring were collected and all samples were analysed by batch analysis on the Roche Cobas e411. Concentrations of CA125, tPSA, CA15‐3 and CA72‐4 showed no significant difference between the natural and stimulated ovarian cycle groups (p≥0.5989). On average the mean PAPP‐A of the natural group was 2.41±0.58 mIU/L higher than the stimulated group (t = 4.10, p < 0.001). CA125 and CA15‐3 results were both significantly influenced by the stage of the cycle (p= In conclusion, batch analysis of all samples from each of the participants was conducted to maximise the possibility that any changes seen in biomarker concentrations were due to biological fluctuations and not because of assay variability. Ovarian stimulation reduced serum PAPP‐A levels, whilst CA125 and CA15‐3 were unaffected by ovarian stimulation per se but showed cyclical changes throughout both natural and stimulated cycles. PAPP‐A, CA125, tPSA and CA15‐3 all showed consistent changes in early pregnancy, and their combined benefits as markers of different aspects of implantation, embryogenesis and placentation warrants further investigation. Only CA125 in early pregnancy crossed the cut‐off associated with disease, ie ovarian cancer, and other gynaecological and inflammatory conditions. Care must therefore be taken when using CA125 determinations to detect disease if the woman is less than 7 weeks pregnant as transient elevations during this time appear normal.

In this thesis a socio-cultural perspective of medical science education is adopted to argue the position that undergraduate medical scientists must be enculturated into the profession as knowledge workers and symbolic analysts who can interact with computers in complex analytical procedures, quality assurance and quality management. The cue for this position is taken from the transformations taking place in the pathology industry due to advances in automation, robotics and informatics. The rise of Evidence-Based Laboratory Medicine (EBLM) is also noted and the observation by higher education researchers, that knowledge systems are transforming in such a way that disciplines can no longer act in isolation. They must now collaborate with disparate fields in transdisciplinary knowledge systems such as EBLM, for which new skills must be cultivated in undergraduate medical scientists. This thesis aims to describe a theoretical basis for knowledge work by taking a semiotic perspective. This is because, semiotics, a theory of signs and representations, can be applied to the structure of transdisciplinary scientific knowledge, the logic of scientific practice and the rhetoric of scientific communications. For this purpose, a semiotic framework is first derived from a wide range of semiotic theories existent in the literature. Then the application of this semiotic framework to clinical chemistry knowledge, context, logic, and rhetoric is demonstrated. This is achieved by interpreting various clinical chemistry data sources, for example, course materials, laboratory spatial arrangements, instruments, printouts, and students' practical reports, collected from a teaching laboratory situation. The results of semiotic analysis indicate that the clinical chemist working in the computerised laboratory environment performs knowledge work, and the term is synonymous with symbolic analysis. It is shown that knowledge work entails the application of a systematic structure for clinical chemistry knowledge derived in terms of the validation procedures applied to laboratory, data, results and tests; the application of logic in the classification and selection of instruments, their rule governed- use, and in troubleshooting errors; pragmatic decisions based on availability of space, services and budgets; discrimination among values in laboratory test evaluations in EBLM, for the cost-effectiveness and relevance of pathology services; and the recognition of rhetorical strategies used to communicate laboratory test information in graphs, charts, and statistics. The role of the laboratory context is also explained through semiotics, in terms of its spatial arrangements and designs of laboratory instruments, as a place that constrains the knowledge work experience. This contextual analysis provides insights into the oppositional trend brought to wide attention by analysts of computerised professional work, that more skills are needed, but that there are fewer highly skilled positions available. The curriculum implications of these findings are considered in terms of the need to cultivate knowledge workers for highly complex symbolic analysis in computerised laboratories; and also the need to prepare medical science graduates for the transdisciplinary knowledge system of EBLM, and related venues of employment such as biomedical research and clinical medicine. In meeting the aims to define and demonstrate knowledge work from the semiotic perspective, this thesis makes an original contribution to knowledge by the application of semiotics to a field in which it has probably never been tested. It contributes to the scholarship of teaching in higher education by formulating a structure for transdisciplinary medical science knowledge, which integrates scientific with other forms of knowledge, and with real world practice.

Abstract In this thesis a socio-cultural perspective of medical science education is adopted to argue the position that undergraduate medical scientists must be enculturated into the profession as knowledge workers and symbolic analysts who can interact with computers in complex analytical procedures, quality assurance and quality management. The cue for this position is taken from the transformations taking place in the pathology industry due to advances in automation, robotics and informatics. The rise of Evidence-Based Laboratory Medicine (EBLM) is also noted and the observation by higher education researchers, that knowledge systems are transforming in such a way that disciplines can no longer act in isolation. They must now collaborate with disparate fields in transdisciplinary knowledge systems such as EBLM, for which new skills must be cultivated in undergraduate medical scientists. This thesis aims to describe a theoretical basis for knowledge work by taking a semiotic perspective. This is because, semiotics, a theory of signs and representations, can be applied to the structure of transdisciplinary scientific knowledge, the logic of scientific practice and the rhetoric of scientific communications. For this purpose, a semiotic framework is first derived from a wide range of semiotic theories existent in the literature. Then the application of this semiotic framework to clinical chemistry knowledge, context, logic, and rhetoric is demonstrated. This is achieved by interpreting various clinical chemistry data sources, for example, course materials, laboratory spatial arrangements, instruments, printouts, and students' practical reports, collected from a teaching laboratory situation. The results of semiotic analysis indicate that the clinical chemist working in the computerised laboratory environment performs knowledge work, and the term is synonymous with symbolic analysis. It is shown that knowledge work entails the application of a systematic structure for clinical chemistry knowledge derived in terms of the validation procedures applied to laboratory, data, results and tests; the application of logic in the classification and selection of instruments, their rulegoverned- use, and in troubleshooting errors; pragmatic decisions based on availability of space, services and budgets; discrimination among values in laboratory test evaluations in EBLM, for the cost-effectiveness and relevance of pathology services; and the recognition of rhetorical strategies used to communicate laboratory test information in graphs, charts, and statistics. The role of the laboratory context is also explained through semiotics, in terms of its spatial arrangements and designs of laboratory instruments, as a place that constrains the knowledge work experience. This contextual analysis provides insights into the oppositional trend brought to wide attention by analysts of computerised professional work, that more skills are needed, but that there are fewer highly skilled positions available. The curriculum implications of these findings are considered in terms of the need to cultivate knowledge workers for highly complex symbolic analysis in computerised laboratories; and also the need to prepare medical science graduates for the transdisciplinary knowledge system of EBLM, and related venues of employment such as biomedical research and clinical medicine. In meeting the aims to define and demonstrate knowledge work from the semiotic perspective, this thesis makes an original contribution to knowledge by the application of semiotics to a field in which it has probably never been tested. It contributes to the scholarship of teaching in higher education by formulating a structure for transdisciplinary medical science knowledge, which integrates scientific with other forms of knowledge, and with real world practice.

Current biophysical studies of membrane proteins are centered on the relation of their structures to key biological functions of membranes in terms of lipid-protein interactions. The conformational transition of rhodopsin from Metarhodopsin I to Metarhodopsin II (Meta I-Meta II) is the triggering event for the visual process. Meta II is the activated form of the visual receptor and binds a signal transducing G protein (transducin), followed by two amplification stages which lead to generation of a visual nerve impulse. Herein, flash photolysis and surface plasmon resonance (SPR) spectroscopy techniques have been used to monitor the Meta I-Meta II transition of rhodopsin in various membrane recombinants. The flash photolysis experiments clearly show a substantial shift to the left of the Meta I-Meta II equilibrium for rhodopsin in egg phosphatidylcholine recombinant membranes. Investigation of the influences on rhodopsin function by non-lamellar forming lipids reveals a characteristic relationship between the Gibbs free energy change for the Meta I-Meta II equilibrium of rhodopsin and the intrinsic curvature of the lipid bilayer. Complementary SPR studies suggest a protrusion of the protein at the activated Meta II state which may be associated with exposure of recognition sites for the signal transducing G protein on the cytoplasmic surface of rhodopsin. All the experimental results obtained here are consistent with the hypothesis of a new flexible surface biomembrane model. The Meta II state is favored by a negative spontaneous curvature of the bilayer, corresponding to an imbalance of the lateral forces within the polar head groups and acyl chains. The mean curvature of membrane bilayer in the Meta II state reflects the small spontaneous curvature of the lipid bilayer in the vicinity of protein. Relief of the lipid curvature frustration in the Meta II state energetically couples the lipids to the photoexcitation of rhodopsin. Consideration of the various energetic contributions suggests the bilayer curvature free energy provides a reservoir of work in the modulation of rhodopsin function in the visual process. These studies that biophysical properties of the liquid-crystalline lipid bilayer are important in relation to protein function and may be relevant to the biomedical investigations of visual dysfunction.

Fler unga människor än någonsin är idag överviktiga och stress och stressrelaterade symptom drabbar idag allt fler unga. Därför är det viktigt att unga människor får kunskaper om hur de på bästa sätt kan ta hand om sig själva.

 Syftet med detta arbete är att undersöka hur elever som läser gymnasiets kurs Idrott och hälsa A ser på den hälsoundervisning de får.

Detta är relevant för alla som arbetar som idrott och hälsa lärare för att kunna hitta en jämkning mellan kursplan och elevernas tankar och förkunskaper.

 Genom intervjuer och fokusintervjuer kom jag fram till att eleverna vill lära sig mer om stress och hur man hanterar stress samt om kost. Eleverna tycker däremot att idrottsläraren inte är rätt person att lära ut kunskaper om tobak.

The low density lipoprotein (LDL) receptor is a transmembrane glycoprotein that mediates the uptake of plasma LDL and thereby provides cholesterol to cells. During its synthesis in the endoplasmic reticulum, the LDL receptor folds and forms disulfide bonds in multiple cysteine-rich repeats. N- and 0-linked oligosaccharide chains are added in the endoplasmic reticulum and processed during passage through the Golgi apparatus, en route to the cell surface. The aim of this thesis was to study the influence of post-translational events on the synthesis of the LDL receptor. Experiments addressed: 1) the necessity of the compartmental organisation of the secretory pathway for the glycosylation of the LDL receptor; 2) the requirements for the formation of disulfide bonds; 3) the role for the chaperone, calnexin, in the folding of the LDL receptor; and 4) the manner in which folding was disrupted by mutations. Experiments were performed in cultured cells that were incubated with [³⁵S]methionine. Biosynthetically-labelled LDL receptor was immunoprecipitated and was analysed by SOS polyacrylamide gel electrophoresis.

The rapid increase in antibiotic resistance demands the identification of novel antibiotics with novel targets. One potential antibacterial target is the biosynthesis of peptidoglycan cell wall, which is both ubiquitous and necessary for bacterial survival. Both the caprazamycin-related compounds A-90289 and muraminomicin, as well as the capuramycin-related compounds A-503083 and A-102395 are potent inhibitors of the translocase I enzyme, one of the key enzymes required for cell wall biosynthesis. The caprazamycin-related compounds contain a core nonproteinogen b-hydroxy-a-amino acid referred to as 5’-C-glycyluridine (GlyU). Residing within the biosynthetic gene clusters of the aforementioned compounds is a shared open reading frame which encodes a putative serine hydroxymethyltransferase (SHMT). The revelation of this shared open reading frame resulted in the proposal that this putative SHMT catalyzes an aldol-type condensation reaction utilizing glycine and uridine-5’-aldehyde, resulting in the GlyU core. The enzyme LipK involved in A-90289 biosynthesis was used as a model to functionally assign this putative SHMT to reveal its functions as an l-threonine: uridine-5’-aldehyde transaldolases. Biochemical analysis indicates enzymatic activity is dependent upon pyridoxal-5’-phosphate, is non-reactive with alternative amino acids, and produces acetaldehyde as a co-product. Structural characterization of the enzymatic product is consistent with (5’S,6’S)-GlyU indicating that this enzyme orchestrates a C-C bond breaking and formation resulting in two new stereocenters to make a new l-a-amino acid. The same activity was demonstrated for the LipK homologues involved in the biosynthesis of muraminomicin, A-503083, and A-102395. This l-threonine: uridine-5’-aldehyde transaldolase was used with alternative aldehyde substrates to prepare unusual l-a-amino acids, suggesting the potential for exploiting this enzyme to make new compounds.

The insulin-like 3 peptide is autocrine/paracrine insulin-related hormone with a size of approximately 6kDa [1]. It mediates through a leucine richG-coupled receptor named LGR8. INSL3 is mainly expressed in human Leydig cells and is directly responsible for migration of the testis during the pre-natal period in maledevelopment. [2]

INSL3 mRNA has recently been verified in human platelets whereas no mRNA has been detected for LGR8 (by Sanofi-Aventis GmbH in Frankfurt,Germany), indicating that INSL3 might be released through paracrine functions at sites of platelet adhesion and aggregation upon a vascular injury.Furthermore, has activated platelets been shown to translate essential proteins upon activation, in a term called “signal-dependent protein synthesis”.The B-Cell lymphoma-3 protein (BCL-3) is an example of such a protein [3], and there is a possibility that INSL3 might be also.

In this thesis we wanted to detect the relaxin- like peptide 3 hormone (INSL3). (Its function, location and the timeframe of its release, when/if it issecreated in stimulated platelets).The source of platelet-derived INSL3 can be found with Western blotting and Enzyme immunoassay.

Detection of the insulin-like 3 peptide in human platelets turned out to be a difficult challenge due to the small amount of INSL3 secretion uponplatelet activation; hence the total amount of INSL3 produced might be below detection limit.

Hollow-fibre liquid-phase microextraction (HF-LPME) was introduced in 1999 as a miniaturised version of liquid-liquid extraction (LLE) in order to reduce the consumption of organic solvents and offer an environmentally-friendly approach to extraction procedures. Since then, several studies have been published in the field of forensic and clinical toxicology applying the technique to a broad range of analytes; however more studies are necessary regarding its applicability to bioanalyses. The principle of HF-LPME is the extraction of analytes across a thin supported liquid membrane within the walls of a hollow fibre from a donor phase (DP) into an acceptor phase (AP). It is an extraction technique that encompasses several parameters that require optimisation for an efficient method; this is most effectively achieved by utilising a design of experiment (DoE) approach rather than the conventional one-factor-at-a-time (OFAT) approach. The main aim of this work is to further investigate the applicability of HF-LPME to the fields of forensic and clinical toxicology by developing and validating methods to extract various drugs from different biological matrices. Complex matrices, such as whole blood, are commonly used in forensic toxicology. Considering that not many studies have been performed on the application of HF-LPME to whole blood (only 10 up to the present day), this is an aspect that requires further investigation. For this, a fast, accurate and precise 3-phase HF-LPME method followed by LC-MS/MS analysis was developed and validated to simultaneously quantify 5 NBOMe drugs in human whole blood. NBOMe drugs are a group of substances part of the so-called “novel psychoactive substances” (NPS); drugs that have been emerging with increasing frequency over the last few years. NBOMes are associated to deaths as the causa mortis, and due to their high potency, these drugs are normally abused in micrograms. For that reason, the HF-LPME method developed had to present high sensitivity (LOD of pg/mL). The aim of the second part of this project was to challenge HF-LPME further by developing and validating methods to assess the potential application of HF-LPME in multi-drug analyses. Urine was selected as biological matrix, and the group of chosen analytes were 14 anti-hypertensive drugs and their metabolites with very different physical-chemical properties. HF-LPME has never been applied to such a broad spectrum of substances in previous bioanalytical studies. These drugs were divided into two groups (acidic and basic/neutral), and a total of four extraction methods (two for each group of analytes) were developed and optimised using chemometrics (DoE) then analysed by LC-MS/MS. Two of these methods were liquid-liquid extraction (LLE) methods that were developed and validated to be used as reference to which the two HF-LPME methods were compared. The LLE methods were sensitive, accurate, precise, and valid for application to real case samples. The HF-LPME methods presented some limitations due to the lack of isotopically-labelled analogues of each specific analyte as internal standards (IS); for non-exhaustive methods the use of these IS should be adopted as standard practise. Real urine samples from genuine patients were extracted using all 4 methods followed by LC-MS/MS analysis. By applying the methods to real case samples, it was possible to define that the HF-LPME methods were suitable for qualitative screening of urine to determine the level of compliance of patients under anti-hypertensive pharmacotherapy. However, for quantification of the drugs applying HF-LPME, further development is required to incorporate the use of isotopically labelled analogues. This study proved that HF-LPME is a potential asset not only for forensic but also for clinical toxicology. It can be a very powerful tool which, mainly due to its green-chemistry approach and pre-concentration capabilities, which allows direct injection into the analytical instrument, could potentially become a more used technique in the future. However, the analyst should be careful when developing HF-LPME methods, to bear in mind its limitations so that methods that are fit-for-purpose can be developed.

Many anticancer therapies, including radiotherapy, act by damaging the deoxyribosenucleic acid (DNA) that is fundamental to cell function and proliferation. H2AX is a histone protein associated with DNA that is phosphorylated to produce γH2AX in response to DNA double strand breaks (DSBs), the most lethal lesions caused in cancer cells. This thesis examines the translation of γH2AX detection assays to clinical situations in order to provide biomarkers of response that might help to guide the treatment of cancer patients. γH2AX immunohistochemistry was developed in preclinical xenograft models, and validated over a range of radiation doses and over time after irradiation. The method was prepared for translation to archived clinical biopsy and surgical specimens. The DSB Biomarkers Pilot Study was established in order to develop a method for γH2AX quantification in direct tumour cell specimens obtained using the clinical technique of fine needle aspiration (FNA) cytology. Eleven patients undergoing anticancer therapy were recruited to the study, and the method evaluated. The coefficient of variation of the measure was 49%. Non-invasive imaging for γH2AX would allow DNA damage to be quantified in all tumour sites, and on multiple occasions. An antibody-based nuclear medicine imaging agent was re-engineered using Fab fragments of the antibody. The novel agent demonstrated improved pharmacokinetics when compared to the whole antibody agent, but reduced target specificity. The findings further develop the potential to exploit DNA damage biomarker measurements in clinical oncology.

Biomarkers are measurable indicators of health status or disease state that can be used for diagnosis and may help guide patient treatment strategies. Enzyme-linked immunosorbent assays (ELISA) and other many clinical techniques currently used for measuring biomarker proteins lack sensitivity, demand high analysis cost, are often not well-suited for measuring multiple biomarkers in a single sample, and require long analysis times. Here, we demonstrate simple, low-cost 3D-printed flow-through devices with integrated electrodes modified with gold nanoparticles (AuNPs) for electrochemical immunoassays of S100B, a biomarker protein related to conditions like skin cancer and brain injuries. Flow-through devices are fabricated from photocurable-resin using a desktop digital light processing (DLP) projector-based 3D printer to produce 500-800 µm square cross-sectional fluidic channels. Threaded ports at the ends and center of the channel are included in the device design for connecting commercially available fittings for fluid delivery and integrating low-cost graphite electrodes for electrochemical biosensing.

The central problem for researchers of HIV-1 evolution is explaining the apparent design of the virus for causing pandemic infection in humans: understanding how HIV-1 spreads is key to halting the pandemic. Current knowledge of how HIV-1 spreads from host to host is based upon experimental observation and indirect inferences informed by theory. The hypothesis of this thesis is that diversity of HIV-1 around the time of transmission is important for viral adaptation to a new human host, rather than intrinsic superiority of particular strains found in infectious fluids from human donor hosts, and that studying recombination is important for understanding this behaviour. To demonstrate the apparent randomness of transmission, I test the null-hypothesis that hard selection accounts for between-host viral divergence in a rare case study of contemporaneous infection. I explain how the experimental data that I have generated and the analyses I have carried out address certain basic assumptions and predictions about HIV-1 transmission and may inform current strategies for vaccine design. Specifically, my approach contributes to the current literature on HIV-1, by investigating an alternative hypothesis to the single virion theory of sexual transmission and by characterizing the role of recombination in a pseudodiploid virus following multiple-infection.

The integrity of an organism's genome depends on the fidelity of DNA replication and the efficiency of DNA repair. The DNA mismatch repair (MMR) system, which is highly conserved from prokaryotes to eukaryotes, plays an important role in maintaining genome stability by correcting base-base mismatches and insertion/deletion (ID) mispairs generated during DNA replication and other DNA transactions. Mismatch recognition is a critical step in MMR. Two mismatch recognition proteins, MutSα (MSH2-MSH6 heterodimer) and MutSβ (MSH2-MSH3 heterodimer), have been identified in eukaryotic cells. MutSα and MutSβ have partially overlapping functions, with MutSα recognizing primarily base-base mismatches and 1-2 nt ID mispairs and MutSβ recognizing 2-16-nt ID heteroduplexes. The goal of this dissertation research was to understand the mechanism underlying differential mismatch recognition by human MutSα and MutSβ and to characterize the unique functions of human MutSα and MutSβ in MMR. In this study, recombinant human MutSα and MutSβ were purified. Binding of the proteins to a T-G mispair and a 2-nt ID mispair was analyzed by gel-mobility assay; ATP/ADP binding was characterized using a UV cross-linking assay; ATPase activity was measured using an ATPase assay; MutSα amd MutSβ’s mismatch repair activity was evaluated using a reconstituted in vitro MMR assay. Our studies revealed that the preferential processing of base-base and ID heteroduplexes by MutSα and MutSβ respectively, is determined by the significant differences in the ATPase and ADP binding activities of MutSα and MutSβ, and the high ratio of MutSα:MutSβ in human cells. Our studies also demonstrated that MutSβ interacts similarly with a (CAG)n hairpin and a mismatch, and that excess MutSβ does not inhibit (CAG)n hairpin repair in vitro. These studies provide insight into the determinants of the differential DNA repair specificity of MutSα and MutSβ, the mechanism of mismatch repair initiation, and the mechanism of (CAG)n hairpin processing and repair, which plays a role in the etiology and progression of several human neurological diseases.

Fibroblast growth factors (FGFs) are a family of growth factors which includes twenty three proteins. FGFs work as modulators for various cellular activities like mitosis, differentiation and survival. Among the FGF family, human fibroblast growth factor-1 (hFGF-1), which is also known as acidic fibroblast growth factor, is a potent angiogenic agent, involved in the formation of new blood vessels in various tissues. hFGF-1 is regarded as a prototype of the FGF family. It serves as one of the potential targets in tumor inhibition and obesity due to its involvement in new blood vessel formation in cancerous regions and adipose tissues. In general, FGFs exert their action by binding to heparin, forming FGF-heparin complex, which can then bind to fibroblast growth factor receptors (FGFRs). Inhibition of FGF dependent signal transduction by heparin mimicking compounds has shown promising results in control and treatment of tumor growth. Naturally occurring glycoside called phloridzin found to have anticancer property. Phloridzin (2-glucoside of phloretin) has structural resemblance to heparin; it is a natural antioxidant, widely known for its antidiabetic activity, besides controlling tumor growth. Phloridzin can mimic heparin and compete with it for FGF binding. This binding can be agonistic or antagonistic in nature on FGF signal transduction. In the present study, we investigated the molecular level interaction between phloridzin and hFGF-1 using various biophysical techniques like steady state fluorescence, limited trypsin digestion and protein-NMR spectroscopy. hFGF-1 needed for the study was expressed in recombinant Escherichia coli cells. The expressed protein was then purified using heparin sepharose affinity chromatography. Both expression and purification were monitored using SDS-PAGE (sodium dodecyl sulfate-polyacrylamide gel electrophoresis). Conformational stability of purified hFGF-1 was assessed through steady state fluorescence. Purified hFGF-1 is in, its native, properly folded conformation. Interaction studies, such as thermal unfolding and limited trypsin digestion were performed to assess the thermal stability and solvent accessibility of hFGF-1 in the presence of phloridzin respectively. It was found from interaction studies that hFGF-1 in the presence of phloridzin shown increased thermal stability and increased resistance against trypsin digestion. In order to locate the sites of interaction on hFGF-1 surface, a protein-NMR study was performed. Exact sites of interaction of phloridzin on hFGF-1 surface were found. In future, isothermal titration calorimetry will be performed to determine kinetics of the enthalpy change and dissociation constant of phloridzin-hFGF-1 interaction. In vivo studies will also be performed after completion of in vitro studies, which will give an insight about possibility of phloridzin and hFGF-1 interaction under physiological condition

Background: Most errors in the venous blood testing process are preanalytical, i.e. they occur before the sample reaches the laboratory. Unlike the laboratory analysis, the preanalytical phase involves several error-prone manual tasks not easily avoided with technological solutions. Despite the importance of the preanalytical phase for a correct test result, little is known about how blood samples are collected in hospitals. Aim: The aim of this thesis was to survey preanalytical procedures in hospitals to identify sources of error. Methods: The first part of this thesis was a questionnaire survey. After a pilot study (Paper I), a questionnaire addressing clinical chemistry testing was completed by venous blood sampling staff (n=314, response rate 94%) in hospital wards and hospital laboratories (Papers II–IV). The second part of this thesis was an experimental study. Haematology, coagulation, platelet function and global coagulation parameters were compared between pneumatic tube-transported samples and samples that had not been transported (Paper V). Results: The results of the questionnaire survey indicate that the desirable procedure for the collection and handling of venous blood samples were not always followed in the wards (Papers II–III). For example, as few as 2.4% of the ward staff reported to always label the test tube immediately before sample collection. Only 22% of the ward staff reported to always use wristbands for patient identification, while 18% reported to always use online laboratory manuals, the only source of updated information. However, a substantial part of the ward staff showed considerable interest in re-education (45%) and willingness to improve routines (44%) for venous blood sampling. Compared to the ward staff, the laboratory staff reported significantly higher proportions of desirable practices regarding test request management, test tube labelling, test information search procedures, and the collection and handling of venous blood samples, but not regarding patient identification. Of the ward staff, only 5.5% had ever filed an error report regarding venous blood sampling, compared to 28% of the laboratory staff (Paper IV). In the experimental study (Paper V), no significant preanalytical effect of pneumatic tube transport was found for most haematology, coagulation and platelet function parameters. However, time-to-clot formation was significantly shorter (16%) in the pneumatic tube-transported samples, indicating an in vitro activation of global coagulation. Conclusions. The questionnaire study of the rated experiences of venous blood sampling ward staff is the first of its kind to survey manual tasks in the preanalytical phase. The results suggest a clinically important risk of preanalytical errors in the surveyed wards. Computerised test request management will eliminate some, but not all, of the identified risks. The better performance reported by the laboratory staff may reflect successful quality improvement initiatives in the laboratories. The current error reporting system needs to be functionally implemented. The experimental study indicates that pneumatic tube transport does not introduce preanalytical errors for regular tests, but manual transport is recommended for analysis with thromboelastographic technique. This thesis underscores the importance of quality improvement in the preanalytical phase of venous blood testing in hospitals.

Iminosugars are a class of small molecules defined by substitution of a sugar’s ring oxygen with nitrogen. Various chemical modifications of these basic structures (e.g. alkyl chain addition off of the ring nitrogen) have been developed during the last several decades. These molecules have been considered as therapeutics for a number of pathologies including viral infection, congenital disorders of glycosylation (of both glycoproteins and glycolipids), and diabetes. This thesis focuses on the application of a small subset of iminosugars, known as deoxynojirimycin derivatives, as therapeutics against dengue virus induced pathology. Dengue virus infection predominates in tropical climates, but autochthonous infection has recently emerged in areas of both southern Europe and the southern United States. With 390 million people infected annually, dengue is the most prevalent arthropod-borne viral infection worldwide, and the possibility of severe pathology including haemorrhage, shock, and/or death, necessitates development of effective antiviral therapies. Although the molecular mechanisms responsible for progression to severe dengue disease are not completely understood, there is considerable evidence for the role of both the innate and the adaptive immune responses in development of life-threatening complications. Excessive activation of the innate immune response, a phenomenon known as cytokine storm, has been hypothesised to explain development of symptoms related to vascular permeability, whereas the adaptive immune response has been implicated in severe disease through two hypotheses – the antibody dependent enhancement and original antigenic sin hypotheses. The evidence regarding each of these potential mechanisms of severe pathology is discussed throughout this thesis principally with respect to how iminosugar treatment could alter any detrimental effects of the immune response to dengue virus infection. The principal aim of this thesis is to consider the potential of deoxynojirimycin iminosugars as antiviral therapeutics in dengue infection with a focus on how these molecules exert their antiviral effects in primary human cells. I first consider the contributions of glycoprotein inhibition and glycolipid inhibition on production of infectious dengue virus. These experiments suggest that inhibition of glycoprotein folding is responsible for inhibition of infectious dengue virus production. I next consider the impact of treatment of a promising clinical candidate iminosugar, N9-methoxynonyl-deoxynojirimycin (MON-DNJ), on the primary human macrophage transcriptome. In uninfected macrophages as well as macrophages infected with dengue virus or treated with lipopolysaccharide to model bacterial sepsis, iminosugar treatment results in activation of the unfolded protein response and inhibition of several elements of the inflammatory response including signalling by the cytokines IFN-γ and TNF-α, and the inflammatory cascade mediated by NF-κB. Activation of the unfolded protein response as a result of treatment with MON-DNJ can be confirmed by analysis of phosphorylated (activated) NFE2L2, a transcription factor that functions principally to control oxidative stress in response to ER stress signals. Modulation of the inflammatory response of macrophages to dengue infection and bacterial sepsis is confirmed by analysis of secreted cytokines. As predicted by my transcriptomic experiments, levels of TNF-α and IFN-γ produced in response to dengue or lipopolysaccharide are reduced by treatment with MON-DNJ. Finally, I attempted to extend these observations to an animal model of dengue infection with a particular focus on TNF receptor and ligand superfamily members. Unfortunately, heterogeneity of cells types from tissue samples as well as limitations of the animal model complicate interpretation of these findings. Nevertheless, this thesis demonstrates that MON-DNJ is an effective dengue antiviral therapeutic and that this therapeutic activity may be related to both reduction of infectious virus as a consequence of inhibition of glycoprotein processing and as a result of changes to the host’s response to the pathogen. These results have been used in part to justify recently initiated clinical trials of MON-DNJ as a dengue antiviral therapy.

RNA-dependent RNA polymerases (RdRps) play a vital role in the life cycle of RNA viruses, being responsible for genome replication and mRNA transcription. In this thesis viral RdRps (vRdRps) of dsRNA bacteriophage phi6 (phi6 RdRp) and Severe Acute Respiratory Syndrome (SARS) coronavirus [non structural protein 12 (NSP-12)] are studied. For SARS polymerase NSP-12, a library-based screening method known as ESPRIT (Expression of Soluble Protein by Random Incremental Truncation) was employed in an attempt to isolate domains of NSP-12 that express solubly in Escherichia coli (E. coli) and are thereby suitable for structural studies. This experiment identified for the first time in a systematic fashion, conditions under which the SARS polymerase could be solubly expressed at small scale and allowed mapping of domain boundaries. Further experiments explored different approaches for increasing expression levels of tractable fragments at large scale. Bacteriophage phi6 RdRp is one of the best studied vRdRps. It initiates RNA synthesis using a de novo mechanism without the need for a primer. Although formation of the de novo initiation complex has been well studied, little is known about the mechanism for the transition from initiation to elongation (i.e. extension of an initiated dinucleotide daughter strand). In the phi6 RdRp initiation complex the C-terminal domain (CTD) blocks the exit path of the newly synthesised dsRNA which must be displaced for the addition of the third nucleotide. The crystal structure of a C-terminally truncated phi6 RdRp (P2T1) reveals the strong non-covalent interactions between the CTD and the main body of the polymerase that must be overcome for the elongation reaction to proceed. Comparing new crystal structures of complexes of both wild-type (WT) and a mutant RdRp (E634 to Q, which removes a salt-bridge between the CTD and main body of the polymerase) with various oligonucleotides (linear and hairpin), nucleoside triphosphates (NTPs) and divalent cations, alongside their biophysical and biochemical properties, provides an insight into the precise molecular details of the transition reaction. Thermal denaturation experiments reveal that Mn2+ acquired from the cell and bound at the phi6 RdRp non-catalytic ion site sufficiently weakens the polymerase structure to facilitate the displacement of the CTD. Our crystallographic and biochemical data also indicate that Mn2+ is released during this displacement and must be replaced for the elongation to proceed. Our data explain the role of the non-catalytic divalent cation in vRdRps and pinpoint the Mn2+-dependent step in viral replication. In addition, by inserting a dysfunctional Mg2+ at the non-catalytic ion site for both WT and E634Q RdRps we captured structures with two NTPs bound within the active site in the absence of Watson-Crick base pairing with template and could map movements of divalent cations during preinitiation through to initiation. Oligonucleotides present on the surface of phi6 RdRp allowed mapping of key residues involved in template entry and unwinding of dsRNA; these preinitiation stages have not been observed previously. Considering the high structural homology of phi6 RdRp with other vRdRps, particularly from (+)ssRNA hepatitis C virus (HCV), insights into the mechanistic and structural details of phi6 RdRp are thought to be relevant to the general understanding of vRdRps.

The rising prevalence of type 2 diabetes (T2D) is a global problem, and suggests that we need better therapeutic strategies against this disease. The glycolytic enzyme glucokinase (GCK) catalyses the phosphorylation of glucose, and is a well-established T2D drug target. Rare GCK mutations cause monogenic beta-cell dysfunction, whilst common genetic variants within GCK are associated with fasting plasma glucose (FPG) levels and T2D risk. Since GCK is expressed in both the pancreas and liver, pharmacological GCK activation provides the promise of a two-pronged attack on hyperglycaemia. In vivo, GCK activity is modulated by the hepatic inhibitor glucokinase regulatory protein (GKRP, gene GCKR). GKRP negatively regulates GCK activity competitively with respect to glucose, and is controlled by fructose 6- and fructose 1-phosphate (F6P and F1P), which compete with each other for binding and enhance or diminish GCK inhibition respectively. GKRP also sequesters GCK in the nucleus and paradoxically stabilises the enzyme. As GCK and its regulatory protein are fundamental to glucose homeostasis, we aimed to investigate the role of genetic variation in both GCK and GCKR to further our understanding of these important T2D drug targets in a system that would be relevant to man. I demonstrated that two novel GCK mutations (T103S and V389L) identified in patients with hyperinsulinaemic hypoglycaemia were kinetically activating and through structural modelling identified a novel regulatory site for GCK activation by small molecular activators. Genome-wide association studies (GWAS) identified GCKR as a regulator of FPG and triglyceride levels, and showed a role for GKRP in T2D risk. Unlike most GWAS hits, this signal included a non-synonymous variant within GCKR (P446L), thus facilitating functional studies. P446L-GKRP was characterised kinetically and at the cellular sequestration-level. This variant showed diminished F6P-mediated modulation, which was proposed to reduce hepatic GCK inhibition, increase glycolytic flux (decreasing FPG), and feed metabolites into liver pathways (elevating triglycerides). As GCKR was not expressed at functional levels within human islets, this phenotype was thought to be driven by the liver. Preliminary analysis at the cellular level was inconclusive, with optimisation required to study human P446L-GKRP in this cellular system. Finally, I showed that mutations within GCKR are not a common cause of “GCK-Like” phenotypes in man, despite the regulatory protein directly modulating GCK activity. These data provide further insight as to the pathogenic consequences of perturbing GCK activity. This must be considered if this enzyme is to be the subject of therapeutic intervention in T2D.

Midazolam (Hypnovel ®) is the only sedating agent used by paramedics at St John Ambulance Service W.A. in the management of many conditions including seizure activities, antisocial or uncontrollable behaviours, back pain incidents and head injuries. Midazolam, with a rapid absorption, fast onset of action and short duration on neurological activity, has been accepted as a safe and effective agent in prehospital treatment since the late-1990s. Often, if a patient is not complying with treatment or is uncontrollable or aggressive, paramedics are required to sedate the individual. This study primarily examines the use of midazolam for the sedation of unmanageable patients who have sustained a head injury in a prehospital setting. The research investigated whether midazolam (n=49) increases the symptoms of hypotension and hypoxia in patients with head injuries in a prehospital selling. Patients that sustained a head injury but did not receive midazolam (n=47) were used as controls. Physiological parameters including blood pressure, pulse and respiration rates, oxygen saturation, along with Coma Scale and Visual Analogue Scale were placed into SPSS analysis package and Excel t-tests. Further analysis on sub divided cohorts of gender, age and severity of head injury was conducted. Results indicated that although significance differences were present, midazolam did not influence hypotension or hypoxia in head injured patients. However the nature of the head injury along with behavioural issues was the result of increased symptoms of hypotension and hypoxia.

The aim of this study was to examine the expression of Thrombomodulin, Tissue Factor, Tissue Factor Pathway Inhibitor and Endothelial Protein C Receptor in placenta throughout the three phases of the third trimester in the normal placenta and in IUGR placenta from full term.

Twenty-five normal placenta samples and twenty-five IUGR placenta samples were obtained and each sample was stained by immunohistochemistry using monoclonal antibodies. Each antibody was optimised for antigen retrieval method and for optimal dilution, before been applied to the test tissue.

The results showed that each of the antibodies mentioned was expressed in normal placenta and in IUGR placenta.

No significant difference could be established concerning the expression of each antibody mentioned between normal and IUGR placenta.

Doctor of Philosophy
Department of Biochemistry and Molecular Biophysics
John M. Tomich
Branched Amphiphilic Peptide Capsules (BAPCs) are peptide nano-spheres comprised of equimolar proportions of two branched peptide sequences bis(FLIVI)-K-KKKK and bis(FLIVIGSII)-K-KKKK that self-assemble in water to form bilayer delimited poly-cationic capsules capable of trapping solutes. We examined the lipid-like properties of this system including assembly, fusion, solute encapsulation, and resizing by membrane extrusion as well as their capability to be maintained at a specific size by storage at 4˚C. These studies along with earlier work from the lab (Gudlur et al. (2012) PLOS ONE 7(9): e45374) demonstrated that the capsules, while sharing many properties with lipid vesicles, were much more robust. We next investigated the stability, size limitations of encapsulation, cellular localization, retention and, bio-distribution of the BAPCs. We demonstrated that the BAPCs are readily taken up by epithelial cells in culture, escape or evade the endocytotic pathway, and accumulate in the peri-nuclear region where they persist without any apparent degradation. The stability and persistence of the capsules suggested they might be useful in delivering radionuclides. The BAPCs encapsulated alpha particle emitting radionuclides without any apparent leakage, were taken up by cells and were retained for extended periods of time. Their potential in this clinical application is being currently pursued. Lastly we studied the temperature dependence of capsule formation by examining the biophysical characteristics of temperature induced conformational changes in BAPCs and examined the structural parameters within the sequences that contribute to their remarkable stability. A region in the nine-residue sequence was identified as the critical element in this process. The ability to prepare stable uniform nano-scale capsules of desired sizes makes BAPCs potentially attractive as delivery vehicles for various solutes/drugs.

DNA methylation is an epigenetic modification that plays an important role in development and differentiation. The patterns of DNA methylation are largely established in early embryogenesis and maintained during development. Abnormal DNA methylation patterns have been associated with many human diseases, including cancer. Despite its importance, little is currently known about the mechanisms that determine DNA methylation patterns throughout the genome. To shed light on the molecular mechanisms that regulate DNA methylation, this study investigates whether DNA methylation patterns are established and maintained normally when human DNA is placed into a heterologous murine environment as opposed to its natural, endogenous chromosomal environment. Here, a previously generated transgenic mouse model, containing 117 kb of human DNA bearing the human α-globin cluster and all of its known regulatory elements, was analysed. The pattern of DNA methylation of the endogenous human α-globin cluster was compared with that of the transgenic cluster in the background of mouse embryonic stem cells (ESCs) and tissues. It was found that, although the normal human DNA methylation pattern was largely established and maintained in a mouse background, the region immediately around the human α-globin genes themselves is generally less methylated in mouse compared to human ESCs. It was found that regions adjacent and up to 2kb from the CpG islands (CGIs), so-called CGI shores, were unusually hypomethylated: this seems to be the result of an extension of CGIs in humanised mouse (hm) ESCs compared to human (h) ESCs. Furthermore, this hypomethylation appeared to increase during development in both erythroid and non-erythoid cells. To identify any cis-regulatory sequences responsible for the hypomethylated state of human CGI shores in the mouse, 2-4 kb human test sequences containing the CGI associated with the human α-globin 2 (α2) gene and its adjacent hypomethylated shore were re-integrated into the mouse α-globin locus via recombination-mediated cassette exchange (RMCE). Human CGI shores became hypomethylated in the context of the re-integrated test sequences, indicating that the appearance of hypomethylation is determined by the underlying human DNA sequence in the test fragments. In summary, the data presented here reveal that human CGIs become extended when placed in a mouse background leading to hypomethylation of human CGI shores in the mouse compared to the pattern of methylation at the normal endogenous human locus. These findings suggest that species-specific factors determine DNA methylation near CGIs. The transgenic mouse model provides an excellent system to dissect out species-specific regulation of CGI shore methylation. Furthermore, this study lays the foundation for future experiments addressing the role of DNA methylation in regulating human gene expression in the murine context, and examining the validity of transgenic mouse models for the study of human gene regulation.

Background: The use of complementary and alternative medicine (CAM) and other non-physician health care providers (dentists, optometrists, etc.) has steadily increased in the United States; however, the associated outcomes reported in the Medicare beneficiary population are limited. Objective: To evaluate the utilization of different healthcare providers by Medicare beneficiaries and assess resultant beneficiary outcomes. Methods: Fourteen outreach events targeting Medicare beneficiaries were conducted throughout Northern/Central California during the 2014 open enrollment period. Trained student pharmacists (working under licensed pharmacist supervision) provided beneficiaries with comprehensive medication therapy management (MTM) services. During each intervention, demographic, quality-of-life, health behavior and health provider/service utilization data were collected. Results: Of 620 respondents, 525 (84%) and 84 (14%) reported using at least one non-physician healthcare professional or CAM provider, respectively. Beneficiaries who reported using non-physician healthcare providers were significantly (p < 0.05) more likely to indicate being ‘very confident’ in managing their chronic health conditions. The number of providers seen with prescriptive authority was positively correlated with the number of prescription medications taken (r s =0.342, p < 0.001). The total number of providers seen was positively correlated with the number of drug-related issues identified (r s = 0.179, p < 0.001). Conclusion: Many beneficiaries have multiple chronic conditions and increasingly utilize a variety of healthcare professionals. As such, bridging the communication chasm between these professionals can improve humanistic outcomes and minimize medication related issues of Medicare beneficiaries. Coordinated care, a key strategy for improving healthcare delivery under the Affordable Care Act, is a step in the right direction.

The Rem, Rem2, Rad, and Gem/Kir GTPases, comprise a novel subfamily of the small Ras-related GTP-binding proteins known as the RGK GTPases, and have been shown to function as potent negative regulators of high voltage-activated (HVA) Ca2+ channels upon overexpression. HVA Ca2+ channels modulate Ca2+ influx in response to membrane depolarization to regulate a wide variety of cellular functions and they minimally consist of a pore-forming α1 subunit, an intracellular β subunit, and a transmembrane complex α2/δ subunit. While the mechanisms underlying RGK-mediated Ca2+ channel regulation remain poorly defined, it appears that both membrane localization and the binding of accessory Ca2+ channel β subunits (CaVβ) are required for suppression of Ca2+ channel currents. We identified a direct interaction between Rem and the L-type Cavα1 C-terminus (CCT), but not the CCT from CaV3.2 T-type channels. Deletion mapping studies suggest that the conserved CB-IQ domain is required for Rem:CCT association, a region known to contribute to both Ca2+-dependent channel inactivation and facilitation through interactions of Ca2+-bound calmodulin (CaM) with the proximal CCT. Furthermore, both Rem2 and Rad GTPases display similar patterns of CCT binding, suggesting that CCT represents a common binding partner for all RGK proteins. While previous studies have found that association of the Rem C-terminus with the plasma membrane is required for channel inhibition, it is not required for CaVβ- subunit binding. However, Rem:CCT association is well correlated with the plasma membrane localization of Rem and more importantly, Rem-mediated channel inhibition upon overexpression. Moreover, co-expression of the proximal CB-IQ containing region of CCT (residues 1507-1669) in HIT-T15 cells partially relieves Rem blockade of ionic current. Interestingly, Ca2+/CaM disrupts Rem:CCT association in vitro. Moreover, CaM overexpression partially relieves Rem-mediated L-type Ca2+ channel inhibition and Rem overexpression alters the kinetics of calcium-dependent inactivation. Together, these data suggest that the association of Rem with the CCT represents a crucial molecular determinant for Rem-mediated L-type Ca2+ channel regulation and provides new insights into this novel channel regulatory process. These studies also suggest that instead of acting as complete Ca2+ channel blockers, RGK proteins may function as endogenous regulators for the channel inactivation machinery.

During the last decades, chemotherapy with cytotoxic drugs has played a significant role in cancer therapy. It’s important to develop new anticancer drugs, and drug sensitivity testing in vitro can be used to find the right diagnosis for the newly developed substances.

The aim of this study was to investigate the cytotoxic activity of the new signal transduction modulators bortezomib, gefitinib and PKC412. The well-established substances cisplatin, cytarabine, doxorubicin and vincristin were investigated for comparison.

The activity of the cytotoxic drugs was analysed in human tumor samples from patients with ovarian carcinoma (n=16) and lymphoma (n=15) by using the Fluorometric Microculture Cytotoxicity Assay (FMCA). The testing of cellular drug resistance by FMCA was accomplished successfully in 33 out of the 34 samples (97%).

The results of this study indicated that the activity of cytotoxic drugs in tumor cells obtained from patients with ovarian carcinoma and lymphoma may be detected by the FMCA. It also suggested that bortezomib and gefitinib could represent promising agents for treatment of ovarian carcinoma and that PKC412 might be of less use for patients with this diagnose.

Trace amounts of pharmaceuticals have been detected in water, from nanograms per liter to micrograms per liter, and have a negatively effect in the aquatic environment and an increased potential risk of drug poisoning for human and animals. In order to address the problem, drug degradation catalyzed by chloroperoxidase (CPO) has been investigated. CPO is a heme-containing glycoprotein secreted by the fungus, Caldariomyces fumago, it catalyzes two major types of oxidations, two one-electron oxidations as catalyzed by most peroxidases and two-electron oxidations which are rare for conventional peroxidases. Five common drugs from a variety of classes which were persistent in the environment have been studied. The metabolites of each drug were identified and the pathways of degradation were proposed. All of them were found to be 100% degradation efficiency in the CPO-H2O2-Cl- system which the catalyzation only required low concentration of CPO (normally nanomolar level) as well as relatively low concentration of H2O2 as cofactor. This degradation method is economic and highly efficient, the results of my experiment extensively support the hypothesis that CPO has a great potential in the environmental application. A new mutant of CPO has been constructed to investigate the role of histidine 105 in the active site of distal pocket. Histidine 105 was suggested to play an essential role in modulating the chlorination activity by forming hydrogen bond with glutamic acid 183, histidine has been replaced by arginine to generate CPO H105R mutant. The construction and transformation were a success but the protein was expressed as apoenzyme, suggesting the mutagenesis to a larger arginine residue at position105 disturbed the heme incorporation.

Klinisk kemiska analyser har hög klinisk relevans. I serum/plasma kan olika parametrar kvantifieras. Dessa parametrar kan vara proteiner, enzymer, joner, metaller, lipider och kolhydrater. Med hjälp av referensintervall kan veterinärer ställa diagnos, följa behandling och sjukdomsförlopp. Parametrar detekteras med olika analysprinciper/metoder; kolorimetri, immunturbidimetri, enzymatisk metod och potentiometri. Djursjukhuset, AniCura, i Hässleholm mottagas både hundar och katter. Cirka 120 kemianalyser analyseras varje dag. AniCura har köpt in ett nytt våtkemiiinstrument, Indiko Plus, som ska ersätta Cobas C111. Med Indiko Plus tillkommer fler provpositioner, 8 nya analyser, ökad kapaciteten och underlättad användning.  Syftet med denna studie var att jämföra instrumenten och ta fram eget referensintervall som jämfördes med referensintervall framtaget av Thermo Fisher. Verifiering av det nya instrumentet genomfördes med precisionsstudie och linjäritetsstudie. Provtagning på hundar och katter utfördes av personal på AniCura. Jämförelsen gjordes med patientprover och referensintervall togs fram med hjälp av prover från friska hundar och katter. Jämförelsen visade att 9 av 13 analyser hade statistisk signifikant skillnad. Orsaken till det beror troligen på skillnaden av reagens, instrumentens ålder och tid mellan mätningar. Ett nytt referensintervall utarbetades och skiljde sig inte mycket från Thermo Fishers intervall. Vidare validering på grund av liten population rekommenderades. Precisionen för Indiko Plus blev godkänd. Linjäriteten blev icke linjär och berodde troligen på en dålig pipett och bör göras om.
Clinical chemical analyzes has high clinical relevance. In serum/plasma, different parameters can be quantified. Parameters can be proteins, enzymes, ions, metals, lipids, and carbohydrates. With reference intervals, veterinarians can set diagnosis, follow treatment and development of the disease. Parameters are detected with different analysis principles/methods; colorimetry, immunoturbidimetry, enzymatic method and potentiometry. The animal hospital, AniCura, in Hässleholm accept dogs and cats. About 120 chemical analyzes are analyzed every day. AniCura purchased a new instrument, Indiko Plus, which will replace Cobas C111. Indiko Plus provide, more sample positions, 8 new analyzes, increased capacity, and facilitated use. The purpose of this study was to compare the instruments and produce a new reference interval which was compared to the reference interval provided by Thermo Fisher. To verify Indiko Plus, a precision and linearity study were conducted. Blood sampling of dogs and cats was performed by staff at AniCura. The comparison was made with patient samples and the reference intervals were obtained using samples from healthy animals. The comparison showed 9 of 13 analyzes had a statistically significant difference. The reason for this is probably due to the difference in reagents, the age of the instruments and the time between measurements. A new reference interval was developed and did not differ much from the Thermo Fisher interval. Further validation due to low population was recommended. The precision for Indiko Plus was approved. The linearity study shows not linear trend but was likely due to a bad pipette and should be redone.

Fibrodysplasia ossificans progressiva (FOP) is a rare autosomal dominant disease resulting in episodic but progressive extraskeletal bone formation. FOP is caused by missense mutations in the cytoplasmic domain of the type I bone morphogenetic protein (BMP) receptor ACVR1, leading to dysregulated activation. Currently there are no available drug treatments and the structural mechanism of mutant activation is still poorly characterised. To address this, a number of BMP and TGFβ receptors, including FOP mutants of ACVR1 were cloned, expressed and purified for both structural and biophysical experiments. The arginine at the site of most recurrent FOP mutation, R206H, is common across all type I receptors except BMPR1A and BMPR1B which have a lysine at this site. The novel structure of BMPR1B differed to wild-type ACVR1 showing some of the conformational changes expected of the active conformation. However, a variety of disease related ACVR1 mutant structures, including ACVR1 R206H, revealed a surprisingly persistent inactive conformation in the kinase domain. Some conformational changes suggestive of activation were observed in the mutant Q207D affecting the ATP pocket, the β4–β5 hairpin and the activation loop. Additionally, the structure of the Q207E mutant showed a slight release of the regulatory glycine-serine rich domain from its inhibitory position. These subtle changes suggest that the mutant inactive conformation is destabilised and potentially more dynamic. In agreement, all of the ACVR1 mutants showed reduced binding to the inhibitory protein FKBP12. However, mutant phosphorylation of the substrate Smad1 was not constitutive, but dependent on the co-expression of the partner ACVR2, consistent with recent evidence from transgenic knock-out mice. A novel 2-aminopyridine inhibitor scaffold with favourable specificity for ACVR1 was identified using a fluorescence-based thermal shift assay. Further derivatives were characterised with improved potency and selectivity. The crystal structures of ACVR1 bound to these inhibitors showed exquisite shape complementarity, contributing to their favourable specificity. This work has increased the understanding of FOP-associated mutant activation and provided a novel starting scaffold for potential drug development.

Aryl hydrocarbon receptor (AHR) is a sensor protein, activated by aromatic chemical species for transcriptionally regulating xenobiotic metabolizing enzymes. AHR is also known to be involved in a variety of pathogenesis such as cancer, diabetes mellitus, cirrhosis, asthma, etc. The AHR signaling induced by xenobiotics has been intensively studied whereas its physiological role in the absence of xenobiotics is poorly understood. Despite a number of ligands of AHR have been reported thus far, further applications are still hampered by the lack of specificity and/or the partially agonistic activity. Thus, a pure AHR antagonist is needed for deciphering the AHR cryptic as well as potential therapeutic agent. The Proteolysis Targeting Chimera (PROTAC) is a bi-functional small molecule containing a ligand and proteolysis inducer. PROTAC recruits the target protein to proteolysis machinery and elicits proteolysis. Thus far, a number of PROTAC have been prepared and demonstrated to effectively induce the degradation of targeted protein in cultured cells, validating PROTAC as a useful research tool. In the present study, PROTACs based on apigenin was prepared and demonstrated to induce the degradation of AHR, providing the proof of concept. To improve activity, a synthetic structure, CH-223191, was optimized for antagonistic activity by positional scanning identifying several AHR antagonists. PROTACs based on the optimal structure were prepared and assessed their biological activity. The products and synthetic scheme described hereby will be helpful for the further understanding on AHR biology as well as for developing therapeutic agents targeting AHR.

Hedgehog (Hh) morphogens play fundamental roles in development whilst dysregulation of Hh signalling leads to disease. Multiple receptors are involved in the modulation of Hh morphogens at the cell surface. Among these, the interactions of Hh ligands with glycosaminoglycan (GAG) (for example heparan or chondroitin sulphate) chains of proteoglycans in the extracellular matrix play a key role in shaping morphogen gradients and fulfil important functions in signal transduction. Several high resolution crystal structures of Sonic Hh (Shh)-GAG complexes have been determined. The interaction determinants, confirmed by binding studies and mutagenesis reveal a novel Hh site for GAG interactions, which appears to be common to all Hh proteins. This novel site is supported by a wealth of published functional data, and resides in a hot spot region previously found to be crucial for Hh receptor binding. Crystal packing analysis combined with analytical ultracentrifugation on Hh-GAG complexes suggest a potential mechanism for GAG-dependent multimerisation. A key step in the Hh pathway is the transduction of the Hh signal into the receiving cell. The Hh signal transducer, Smoothened, is a key target drug target in the pathway with several modulators in clinical trials, despite an absence of structural data. Smoothened is required to activate all levels of Hh signalling. Recent evidence points to the conserved N-terminal ectodomain (ECD) in regulating Smo activity, from vertebrates to invertebrates. Despite the central importance of the ECD, its precise function remains elusive. A crystal structure of the ECD at 2.2 Å resolution is reported here. Structural analysis and biophysical experiments are discussed with reference to the potential function of this intriguing domain.

The low redox potential of guanines (G 1.29 V vs. NHE) compared to other nucleobases, makes them potentially susceptible to attack by exogenous and endogenous damaging species. This property of guanine has also been utilized for the development of several anticancer agents including the well-known platinum complexes, cisplatin and carboplatin. The two closely related nickel complexes, NiCR and NiCR-2H, exhibit significant differences in cytotoxicity towards MCF-7 cancer cells. In the first part of this work, we explain this difference using biochemical and biophysical approaches to study their interactions with duplex DNA. The nickel complexes were found to selectively oxidize guanines in bulged DNA structures in the presence of oxidant and notably NiCR-2H oxidizes guanines more efficiently than NiCR. According to 1 H NMR studies, NiCR-2H binds strongly to the N7 position of dGMP compared to NiCR and could be an important oxidation product of NiCR under physiological conditions. The second part of this work focuses on the secondary DNA structures known as G-quadruplex formed in the guanine rich telomeric region. G-quadruplex is formed by stacking of G-quartets (a coplanar cyclic array of four Gs) on top of each other. Its formation is known to inhibit the activity of the reverse transcriptase telomerase that is overexpressed in 80-90% cancer cells. The guanines in telomeric DNA are readily oxidized due to their low redox potential and the major oxidation product is 7, 8-dihydro-8-oxoguanine (OxodG). OxodG (0.58 V vs. NHE) can further be oxidized in the presence of one electron oxidants and the resulting product forms adducts with endogenous nucleophiles such as spermine. In light of these findings, we hereby designed and synthesized novel bifunctional perylene derivatives that can selectively bind to the telomeric DNA via G-quadruplex formation and subsequently react with OxodG in close proximity. These compounds have strong binding affinity towards G-quadruplex and can significantly stabilize the OxodG containing G-quadruplex motif by end stacking on the upper G-quartet. The effect of these compounds on telomerase activity and cytotoxicity towards Hep3B cancer cells was also evaluated.

Peptide tags are ubiquitous in the life sciences, with roles including purification and selective labeling of proteins. Because peptide tags are small they have a limited surface area for binding and hence usually form low affinity protein interactions. These weak interactions limit the uses of peptide tags in cases that require resistance to forces generated with macromolecular architectures or protein motors. Hence a way to create a covalent interaction with a peptide tag would be useful. It was found possible to create a covalent bond-forming peptide tag using the spontaneous isopeptide chemistry of the CnaB2 domain from the Gram-positive bacterium Streptococcus pyogenes. In the CnaB2 domain a reactive Lysine forms an isopeptide bond with an Aspartic acid, catalyzed by a Glutamic acid, creating an internal covalent linkage. Subsequently it was shown that the CnaB2 domain could be split into two parts, a domain with the Lysine and Glutamic acid called SpyCatcher and a peptide with the Aspartic acid called SpyTag, such that the isopeptide covalent linkage can be formed when SpyCatcher/SpyTag are mixed together. SpyCatcher/SpyTag was applied in this thesis and showed functionality in a wide array of scenarios. SpyCatcher/SpyTag covalently linked within the cytosol of E. coli, on surface membrane proteins of HeLa cells, and regardless of whether SpyTag was located on the N- or C-terminus or an internal site. Crystal structures of SpyCatcher/SpyTag were then obtained and it was found possible to shrink the SpyCatcher by 32 residues to a core domain of 83 residues. To create an even smaller covalent linkage system, SpyCatcher was split further to generate a protein (SpyLigase) ligating two peptide tags. The β-sheet with the reactive Lysine was removed from SpyCatcher and called KTag. SpyLigase could covalently link SpyTag and KTag. SpyLigase-induced ligation was independent of the location of SpyTag/KTag on the target proteins and was applied to create affibody polymers, which were shown to improve magnetic isolation of cells with low tumor antigen expression. Through this work protein-protein covalent linkage systems were refined and generated that have future applications for the creation of unique macromolecular structures, cellular labeling, and protein cyclization.

Current research shows moderate alcohol consumption is associated with decreased risk of diabetes and excessive consumption or binge drinking can cause insulin resistance and diabetes. In 2010, diabetes was the seventh leading cause of death in the United Statesand was responsible for significant health complications: blindness, kidney failure, and limb amputations, and is a large national economic burden. Fasting blood glucose (FBG) is a tool used to help diagnose diabetes. Abnormally high FBG, ≥100 mg/dl, is indicative of diabetes and pre-diabetes. Few studies have observed diabetic prevalence among young adults or college students. Studying young adults can help provide added information about early risk factors for diabetes and pre-diabetes, facilitating public health efforts to stem the rising tide of the diabetes epidemic. This study aimed to research the associations between alcohol consumption (numbers of days alcohol consumed in the past month and binge alcohol consumption in the past month) and FBG in a college population as part of the FLASH cohort study. FBG levels were measured in 141 young adult participants and alcohol consumption was determined by self report. Other individual-level characteristics and potential confounding variables were also collected. The association between alcohol consumption and FBG followed a J-shaped curve whereby students who reported drinking 6-8 days within the last 30 days showed significantly lower FBG levels than those who did not drink and those who consumed alcohol on nine or more days (p=0.04). Binge drinking did not have a significant association with FBG (p=0.4). Sex and body mass index were also significantly associated with FBG. In conclusion, moderate frequency of alcohol consumption is found to have an inverse relationship with FBG and excessive drinking can reverse these effects.

The thesis describes utilizing mass spectrometry and computational methods to study two groups of molecular systems: small organic molecules and oligopeptides. The gas-phase acidities were measured and the structures of the molecular species were calculated. The small molecules investigated included methylparaben, ibuprofen, and triclosan, all known to have some biological activity. The gas-phase acidity measurements made for these small molecules had the solvent and collisional gas pressures adjusted in order to observe their potential influences. The results obtained provide insight into the ion chemistry of these molecules and how the energetics may change the observed behavior of the ion as well as the resulting thermochemical properties measured. The oligopeptides studied were a family of tri-peptides in which a cysteine probe was placed within an alanine backbone. The cysteine probe was either in the L- or D- configuration in order to detect any fundamental differences among the diastereotopic peptides. Compared to the L-cysteine isomers, the D-cysteine peptides appear to display a change in gas-phase behavior and their respective dissociation profiles. These changes may have an implication of altering the biochemical properties when chirality changes in biological systems.

Laboratory analyses, essential in screening, diagnosis, treatment, and monitoring of disease, are indispensable in health care, but appropriate utilization is intricate. The overall aim of this thesis was to study the use of laboratory tests in Sweden with the objective to evaluate and optimize test utilization. Considerable inter-county variations in test utilization in primary health care in Sweden were found; variations likely influenced by local traditions and habits of test ordering leading to over- as well as underutilization. Optimized test utilization was demonstrated to convey improved quality and substantial cost savings. It was further established that continuing medical education is a suitable means of optimizing test utilization, and consequently enhancing quality and cost-efficiency, as such education was demonstrated to achieve long-lasting improvements in the test ordering habits of primary health care physicians. Laboratory tests are closely associated with other, greater, health care costs, but their indirect effects on other areas of medicine are rarely evaluated or measured in monetary terms. In an illustrative example of the effects that optimal test utilization may have on associated health care costs it was demonstrated that F-calprotectin, a fecal marker of intestinal inflammation, has the potential to substantially reduce the number of invasive investigations necessary in, and the costs associated with, the diagnosis of Inflammatory Bowel Disease. Information on trends in test utilization is essential to optimal financial management of laboratories. A longitudinal evaluation revealed that test utilization had increased by 70% in 6 years, and even though the selection of tests more than doubled, a very small number of tests represented a stable, and disproportionally large, share of the total number of tests ordered. The study defines trends and thus has potential predictive values. In summary, appropriate utilization of laboratory analyses has both clinical and economical benefits on all levels of health care.

Peptides have attracted increasing attention as therapeutics in recent years, at least partially as a consequence of the widespread acceptance of protein therapeutics; but also as possible solutions to problems such as short half-life and delivery of molecules, and as therapeutics in their own right. The current work presents three projects that involve applications of peptides in a therapeutic environment. The first project studies the use of ER retaining peptides and CPPs (Cell penetrating peptides) in enhancing the effective concentration of DNJ (1-deoxynojirimycin), an α-glucosidase inhibitor, in cells. DNJ constructs with ER retaining peptides (6-[N-(1-deoxynojirimycino)]-hexanoyl-KDEL and 6-[N-(1-deoxynojirimycino)]-hexanoyl-KKAA) and CPPs (6-[N-(1-deoxynojirimycino)]-hexanoyl-TAT and 6-[N-(1-deoxynojirimycino)]-hexanoyl-MAP) were synthesised and analysed for their inhibitory activity against α-glucosidase I and II in vitro. The constructs were then analysed in a cell-based assay to determine their inhibitory activity on α¬-glucosidase-mediated hydrolysis of N-linked oligosaccharides. FITC-labelled ER retaining peptides were also synthesised to determine the internalisation and trafficking of the constructs by FACS and IF-microscopy. While none of the DNJ-constructs showed higher cellular inhibition than NB-DNJ (N-butyl DNJ; Miglustat), the CPP construct 6-[N-(1-deoxynojirimycino)]-hexanoyl-TAT showed comparable activity and the ER retaining construct 6-[N-(1-deoxynojirimycino)]-hexanoyl-KDEL showed a small but significant increase in activity following long-term administration. The second project focuses on beauveriolides, a cyclic depsipeptide family shown to have activity as ACAT inhibitors and thus a possible treatment for Alzheimer’s disease by the decrease in the production of Amyloid β (Aβ). A published total synthetic method was improved by the use of a cross-metathesis to reduce the total synthesis by 5 steps and increase its flexibility to allow the production of analogues. The synthesised beauveriolide III was used in attempts to develop an IF-FACS-based assay to measure the intracellular concentrations of Aβ. However, the location of γ-secretase in the used cell-line meant that levels of intracellular Aβ were not sufficient to track any decrease caused by ACAT inhibition. The third project involves the design of a cyclic peptide that could block the binding site for the influenza virus in the host cell. The cyclic peptide (cGSGRGYGRGWGVGA) was developed from a comparative study of four different sialic acid-binding proteins and synthesised by solution cyclisation of the linear peptide synthesised by traditional solid phase peptide synthesis (SPPS). An in silico study showed that the cyclic peptide allowed overlap with the binding site of Hemagglutinin. A 1H NMR titration determined the dissociation constant of the cyclic peptide to sialic acid. The KD corresponded to a low binding affinity, however the observed binding seemed to be specific and caused by a single bound conformation.

Connor O’Hara July 29, 2019 Inhibition of Cancer Stem Cells by Glycosaminoglycan Mimetics In the United States cancer is the second leading cause of death, with colorectal cancer (CRC) being the third deadliest cancer and expected to cause over 51,000 fatalities in 2019 alone.1 The current standard of care for CRC depends largely on the staging, location, and presence of metastasis.2 As the tumor grows and invades nearby lymph tissue and blood vessels, CRC has the opportunity to invade not only nearby tissue but also metastasize into the liver and lung (most commonly).3 The 5-year survival rate for metastasized CRC is <15%, and standard of care chemotherapy regimens utilizing combination treatments only marginally improve survival.3-5 Additionally, patients who have gone into remission from late-stage CRC have a high risk of recurrence despite advances in treatment.6-7 The Cancer Stem-like Cell (CSC) paradigm has grown over the last 20 years to become a unifying hypothesis to support the growth and relapse of tumors previously regressed from chemotherapy (Figure 1).8 The paradigm emphasizes the heterogeneity of a tumor and its microenvironment, proposing that a small subset of cells in the tumor are the source of tumorigenesis with features akin to normal stem cells.9 The CSCs normally in a quiescent state survive this chemotherapy and “seed” tumor redevelopment.10 First observed in acute myeloid lymphoma models, CSCs have since been identified in various other cancers (to include CRC) by their cell surface antigens and unique properties characterizing them from normal cancer cells.11-12 These include tumor initiation, limitless self-renewal capacity to generate clonal daughter cells, as well as phenotypically diverse, mature, and highly differentiated progeny.13-14 Previously our lab has identified a novel molecule called G2.2 (Figure 2) from a unique library of sulfated compounds showing selective and potent inhibition of colorectal CSCs in-vitro.15 G2.2 is a mimetic of glycosaminoglycans (GAGs) and belongs to a class of molecules called non-saccharide GAG mimetics (NSGMs). Using a novel dual-screening platform, comparisons were made on the potency of G2.2 in bulk monolayer cells, primary 3D tumor spheroids of the same cell line, and subsequent generations of tumor spheroids. This work has shown in-vitro the fold-enhancement of CSCs when culturing as 3D tumor spheroids. Spheroid culture serves as a more accurate model for the physiological conditions of a tumor, as well as the functional importance of upregulating CSCs. Evaluation of G2.2 and other NSGMs was performed in only a few cell lines, developing a need to better understand the ability of G2.2 to inhibit spheroids from a more diverse panel of cancer cells to better understand G2.2’s mechanism. The last few decades have seen the advancement in fundamental biological and biochemical knowledge of tumor cell biology and genetics.16 CRC, in particular, has served as a useful preclinical model in recapitulating patient tumor heterogeneity in-vitro.17 Recent work has characterized the molecular phenotypes of CRC cell lines in a multi-omics analysis, stratifying them into 4 clinically robust and relevant consensus molecular subtypes (CMS).18-19 Our work was directed to screen a panel of cells from each of the molecular subtypes and characterize the action of G2.2 and 2nd generation lipid-modified analogs, synthesized to improve the pharmacokinetic properties of the parent compound. Four NSGMs, namely G2.2, G2C, G5C, and G8C (Figure 2) were studied for their ability to inhibit the growth of primary spheroids across a phenotypically diverse panel. Compound HT-29 IC50 (μM) Panel Average IC50 (μM) G2.2 28 ± 1 185 ± 55 G2C 5 ± 2 16 ± 15 G5C 8 ± 2 63 ± 19 G8C 0.7 ± 0.2 6 ± 3 Primary spheroid inhibition assays were performed comparing the potency of new NSGMs to G2.2. Fifteen cell lines were evaluated in a panel of colorectal adenocarcinoma cell lines with several cell lines representing each CMS. Primary spheroid inhibition assays revealed 3 distinct response with regard to G2.2’s ability to inhibit spheroid growth. Cells from CMS 3 and 4, which display poor clinical prognosis, metabolic dysregulation, and enhanced activation of CSC pathways, showed the most sensitivity to G2.2 (mean IC50 = 89 ± 55 μM). Mesenchymal CMS 4 cell lines were over 3-fold more sensitive to treatment with G2.2 when compared to CMS 1 cell lines. Resistant cell lines were composed entirely of CMS 1 and 2 (mean IC50 = 267 ± 105 μM). In contrast, all lipid-modified analogs showed greater potency than the parent NSGM in almost every CRC cell line. Of the three analogs, G8C showed the greatest potency with a mean IC50 of less than 15 μM. Of the CRC spheroids studied, HT-29 (CMS 3) was most sensitive to G8C (IC50 = 0.73 μM). To evaluate the selectivity of NSGMs for CSC spheroid inhibition, MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium) cytotoxicity assays were performed on monolayer cell culture, and the fold-selectivity of NSGM for spheroids was analyzed. Data shows that NSGMs preferentially target CSC-rich spheroids compared with monolayer cellular growth, with G2.2 having over 7-fold selectivity for spheroid conditions. This fold selectivity was enhanced in CMS 3/4, supporting the idea that G2.2 targets a mesenchymal and stem-like phenotype. To further validate this selectivity, limiting dilution assays were performed across the panel to determine the tumor-initiating capacity of each cell line. Cell lines which showed a sensitive response to G2.2 were over 2-fold more likely to develop into spheroids, validating the previous hypothesis. Further characterization was performed analyzing the changes G2.2 induced on CSC markers, as well as the basal expression of a unique pair of cancer cells. Western blots showed a reduction in self-renewal marker across all CMS after treatment with G2.2, and that cell lines sensitive to G2.2-treatment overexpress mesenchymal and stem-like markers. G2.2-resistant cell lines show an epithelial phenotype, lacking this expression. The positive results observed in these studies enhance the understanding of G2.2 and analogs, and further evaluation with additional cell lines of various tissues would improve the knowledge thus far gained. However, all experiments described take valuable time to perform and analyze. Thus, there became a need to develop a high-throughput screening (HTS) platform for our assays that standardized analysis and enhanced productivity. Initial development of the method for this assay are underway, and recent evidence from these evaluations of breast cancer spheroids suggests that G2.2 and analogs may be tissue-specific compounds for the treatment of cancer. Future work entails refining the application of this method for evaluation of the NCI-60 (National Cancer Institute) tumor cell panel. Overall, these results make several suggestions concerning the NSGMs evaluated against the panel. First, G2.2 selectively targets CSCs with limited toxicity to monolayer cells of the same cell line. Further, G2.2 has the greatest potency with CMS 3/4, whose mesenchymal phenotypes are associated with poor clinical prognosis and enrichment of CSCs. Supporting evidence include that sensitive cell lines are highly tumorigenic and show enhanced expression of mesenchymal/CSC markers compared to resistant cell lines. Lipid-modification of G2.2 enhances in-vitro potency against spheroid growth, with nM potency reached in the most sensitive cell lines. Evidence in the development of a HTS platform also suggests these NSGMs show tissue specificity to cancers of the intestine. Further work characterizing the mechanism of NSGMs in a broader multi-tissue panel will enhance our understanding of the compounds as a potential therapy to dramatically improve patient survival through specific targeting of tumorigenesis. References 1. Colorectal Cancer Facts & Figures 2017-2019. American Cancer Society 2017. 2. Compton, C. C.; Byrd, D. R.; Garcia-Aguilar, J.; Kurtzman, S. H.; Olawaiye, A.; Washington, M. K. Colon and rectum. In AJCC Cancer Staging Atlas, 2nd ed.; Ed. Springer Science: New York, 2012; pp 185–201. 3. Van Cutsem, E.; Cervantes, A.; Adam, R.; Sobrero, A.; Van Krieken, J. H.; Aderka, D.; Aranda Aguilar, E.; Bardelli, A.; Benson, A.; Bodoky, G.; et al. ESMO consensus guidelines for the management of patients with metastatic colorectal cancer. Ann. Oncol. 2016, 27, 1386–422. 4. Siegel, R. L.; Miller, K. D.; Fedewa, S. A.; Ahnen, D. J.; Meester, R. G. S.; Barzi, A.; Jemal, A. Colorectal cancer statistics, 2017. CA Cancer J. Clin. 2017, 67, 177–193. 5. Moriarity, A.; O'Sullivan, J.; Kennedy, J.; Mehigan, B.; McCormick, P. Current targeted therapies in the treatment of advanced colorectal cancer: a review. Ther. Adv. Med. Oncol. 2016, 8, 276–293. 6. Seidel, J.; Farber, E.; Baumbach, R.; Cordruwisch, W.; Bohmler, U.; Feyerabend, B.; Faiss, S. Complication and local recurrence rate after endoscopic resection of large high-risk colorectal adenomas of >/=3 cm in size. Int. J. Colorectal Dis. 2016, 31, 603–611. 7. Pugh, S. A.; Shinkins, B.; Fuller, A.; Mellor, J.; Mant, D.; Primrose, J. N. Site and stage of colorectal cancer influence the likelihood and distribution of disease recurrence and postrecurrence survival: data from the FACS randomized controlled trial. Ann. Surg. 2016, 263, 1143–1147. 8. Batlle, E.; Clevers, H. Cancer stem cells revisited. Nat. Med. 2017, 23, 1124–1134. 9. Hanahan, D.; Weinberg, R. A. Hallmarks of cancer: the next generation. Cell 2011, 144, 646–674. 10. Tirino, V.; Desiderio, V.; Paino, F.; De Rosa, A.; Papaccio, F.; La Noce, M.; Laino, L.; De Francesco, F.; Papaccio, G. Cancer stem cells in solid tumors: an overview and new approaches for their isolation and characterization. FASEB J. 2013, 27, 13–24. 11. Bonnet, D.; Dick, J. E. Human acute myeloid leukemia is organized as a hierarchy that originates from a primitive hematopoietic cell. Nat. Med. 1997, 3, 730–737. 12. Desai, A.; Yan, Y.; Gerson, S. L. Concise reviews: cancer stem cell targeted therapies: toward clinical success. Stem Cells Transl. Med. 2019, 8, 75–81. 13. Munro, M. J.; Wickremesekera, S. K.; Peng, L.; Tan, S. T.; Itinteang, T. Cancer stem cells in colorectal cancer: a review. J. Clin. Pathol. 2018, 71, 110–116. 14. Zhou, Y.; Xia, L.; Wang, H.; Oyang, L.; Su, M.; Liu, Q.; Lin, J.; Tan, S.; Tian, Y.; Liao, Q.; Cao, D. Cancer stem cells in progression of colorectal cancer. Oncotarget 2018, 9, 33403–33415. 15. Patel, N. J.; Karuturi, R.; Al-Horani, R. A.; Baranwal, S.; Patel, J.; Desai, U. R.; Patel, B. B. Synthetic, non-saccharide, glycosaminoglycan mimetics selectively target colon cancer stem cells. ACS Chem. Biol. 2014, 9, 1826–1833. 16. Punt, C. J.; Koopman, M.; Vermeulen, L. From tumour heterogeneity to advances in precision treatment of colorectal cancer. Nat. Rev. Clin. Oncol. 2017, 14, 235–246. 17. Mouradov, D.; Sloggett, C.; Jorissen, R. N.; Love, C. G.; Li, S.; Burgess, A. W.; Arango, D.; Strausberg, R. L.; Buchanan, D.; Wormald, S.; et al. Colorectal cancer cell lines are representative models of the main molecular subtypes of primary cancer. Cancer Res. 2014, 74, 3238–3247. 18. Guinney, J.; Dienstmann, R.; Wang, X.; de Reynies, A.; Schlicker, A.; Soneson, C.; Marisa, L.; Roepman, P.; Nyamundanda, G.; Angelino, P.; et al. The consensus molecular subtypes of colorectal cancer. Nat. Med. 2015, 21, 1350–1356. 19. Berg, K. C. G.; Eide, P. W.; Eilertsen, I. A.; Johannessen, B.; Bruun, J.; Danielsen, S. A.; Bjornslett, M.; Meza-Zepeda, L. A.; Eknaes, M.; Lind, G. E.; et al. Multi-omics of 34 colorectal cancer cell lines - a resource for biomedical studies. Mol. Cancer 2017, 16, 116–132.

La gestió del risc és una activitat que s’ha anat introduint al laboratori clínic en els darrers anys. Una de les eines més utilitzades per al seu estudi és l’Anàlisi Modal de Fallades i Efectes (AMFE), però té l’inconvenient d’utilitzar escales subjectives per realitzar la caracterització dels errors a partir de la valoració de la seva probabilitat d’aparició, gravetat i capacitat de detecció. Una altra eina, la mètrica Sigma, permet avaluar, a partir dels errors detectats, el rendiment d’un procés d’una manera objectiva i quantitativa, utilitzant una escala internacionalment reconeguda. En aquesta Tesi, s’han utilitzat les dues eines per a la gestió dels riscos del procés analític del Programa de Cribratge Neonatal de Catalunya, al llarg dels anys 2016-2018, a la seqüència metodològica que es descriu a continuació. En primer lloc, l’aplicació de l’AMFE i de la mètrica Sigma han permès avaluar els possibles errors potencials, al llarg de tot el procés analític del Programa, calculant el Número de Priorització del Risc (NPR) mitjançant l’AMFE i el valor de Sigma () a partir de la freqüència d’aparició de cada error expressada com a Defectes Per Milió d’Oportunitats (DPMO). En segon lloc, s’ha determinat el grau de concordança de la informació que ofereixen les dues metodologies establint una correspondència quant als valors i significat dels resultats obtinguts amb cada una d’elles. El resultat s’ha utilitzat per establir l’acceptació o no del risc i quan cal introduir millores. Els resultats finals de l’estudi mostren que s’han detectat 48 riscos al llarg del procés analític del Programa de Cribratge Neonatal: 14 a la fase pre pre analítica, 6 a la fase pre analítica, 22 a la fase analítica, 5 a la fase post analítica i 1 a la fase post post analítica. En 14 riscos es va trobar que no existia una concordança entre els resultats de les dues metodologies, i precisaven d’un seguiment acurat de cadascun d’ells per prendre la decisió més convenient. De la resta, 27 riscos es van considerar residuals i no calia fer cap acció de millora perquè els valors de NPR i de Sigma () es trobaven en el marge acceptable establert, però 6 riscos no eren acceptables i requerien la introducció d’accions de millora. Aquests 6 riscos es distribuïen de la següent manera: 4 riscos a la fase pre pre analítica, 1 risc a la fase analítica i 1risc a la fase post analítica. Ha estat el laboratori o bé l’Agència de Salut Pública de Catalunya, d’acord amb els responsables del laboratori, els encarregats d’establir les accions de millora amb l’objectiu de mitigar o eliminar aquests riscos. Per demostrar que la metodologia desenvolupada pot ser d’aplicació en d’altres àmbits del laboratori clínic, es mostren els resultats de la seva aplicació a les fases extra analítiques dels processos analítics del Centre de Diagnòstic Biomèdic. S’han detectat 14 riscos a la fase pre pre analítica en què existeix una concordança entre els resultats del NPR de l’AMFE i el valor de Sigma (). En tots els casos es tracta de riscos menors i residuals. A partir dels resultats obtinguts es mostra que la metodologia que es proposa pot ser de gran utilitat per a la gestió dels riscos de qualsevol activitat del laboratori clínic i que les eines utilitzades (AMFE i Sigma) ofereixen informació complementària: amb l’AMFE a més de la priorització dels riscos, es posa de manifest la gravetat i la capacitat de detecció d’un error potencial mentre que la mètrica Sigma dóna idea del rendiment del procés.
Risk management has been introduced in clinical laboratories in recent years. Failure Modes and Effects Analysis (FMEA) and Sigma metrics have been used for the risk management of the analytical process of the Neonatal Screening Program of Catalonia from 2016 to 2018. The methodological sequence that has been used was: firstly, the application of FMEA and Sigma metrics; secondly, the establishment of a correspondence of the degree of agreement of the information provided by the two methodologies, and finally, the criteria to decide whether or not to accept the risk have been defined The results of the study show that 48 risks have been detected throughout the analytical process of the Neonatal Screening Program: 14 in the pre-pre-analytical phase, 6 in the pre-analytical phase, 22 in the analytical phase, 5 in the post-analytical phase and 1 in the post-post-analytical phase. It was found that in 14 risks there was no agreement between the results of the NPR provided by the FMEA and the Sigma value. Another 28 were considered marginal risks and improvement actions were not required. A further 6 risks were classified as not acceptable risks and required the introduction of improvement actions and were distributed as follows: 4 in the pre-analytical phase; 1 in the analytical phase and 1 in the post-analytical phase. It has been the laboratory or the Public Health Agency of Catalonia (in agreement with laboratory staff), who established the improvement actions with the aim of mitigating or eliminating the risks. In order to demonstrate that the developed methodology may be applicable in other areas of the clinical laboratory, results of its application to the extra-analytical phases of the analytical processes carried out at the Biomedical Diagnostic Centre are also shown. These results show that the proposed methodology can be useful for the risk management of any activity undertaken in a clinical laboratory. Moreover, FMEA and Sigma metric tools give complementary information in addition to risk prioritization. FMEA highlights the severity and ability to detect a potential error, while Sigma metrics provide an idea of process performance.

Background Venous blood tests constitute an important part in the diagnosis and treatment of patients. However, test results are often viewed as objective values rather than the end result of a complex process. This has clinical importance since most errors arise before the sample reaches the laboratory. Such preanalytical errors affect patient safety and are often due to human mistakes in the collection and handling of the sample. The preanalytical performance of venous blood testing in primary health care, where the majority of the patients contact with care occurs, has not previously been reported. Aims To investigate venous blood sampling practices and the prevalence of haemolysed blood samples in primary health care. Methods A questionnaire investigated the collection and handling of venous blood samples in primary health care centres in two county councils and in two hospital clinical laboratories. Haemolysis index was used to evaluate the prevalence of haemolysed blood samples sent from primary health care centres, nursing homes and a hospital emergency department. Results and discussion The results indicate that recommended preanalytical procedures were not always followed in the surveyed primary health care centres. For example, only 54% reported to always use name and Swedish identification number, and 5% to use photo-ID, the two recommended means for patient identification. Only 12% reported to always label the test tubes prior to blood collection. This increases the possibility of sample mix-up. As few as 6% reported to always allow the patient to rest at least 15 minutes before blood collection, desirable for a correct test result. Only 31% reported to have filed an incident report regarding venous blood sampling, indicating underreporting of incidents in the preanalytical phase. Major differences in the prevalence of haemolysed blood samples were found. For example, samples collected in the primary health care centre with the highest prevalence of haemolysed samples were six times (95% CI 4.0 to 9.2) more often haemolysed compared to the centre with the lowest prevalence. The significant variation in haemolysed samples is likely to reflect varying preanalytical conditions. Conclusions This thesis indicates that the preanalytical procedure in primary health care is associated with an increased risk of errors with consequences for patient safety and care. Monitoring of haemolysis index could be a valuable tool for estimating preanalytical sample quality. Further studies and interventions aimed at the preanalytical phase in primary health care are clearly needed.

In addition to a central circadian clock in the suprachiasmatic nucleus (SCN), zebrafish (Danio rerio) have local clock systems in their peripheral tissues. These peripheral tissues express a complement of clock genes that can be synchronized with the 24 h light/dark cycle and thus may be entrained by light. To date, teleost multiple tissue (tmt) opsin identified from Fugu rubripes and Danio rerio is the only opsin that has been proposed as a candidate to mediate this cellular photoentrainment (Moutsaki et al., 2003). Here we report the discovery of a multigene family of tmt opsins found not only in the teleost fishes, but in vertebrates,including amphibians, birds, reptiles, and some mammals. Phylogenetic analysis demonstrated that this gene family consists of three main classes, tmtI, tmtII and tmtIII, with each duplicating further to give two paralogues in the zebrafish genome. Their predicted amino acid sequences contain most of the characteristic features for the function of a photopigment opsin, as well as seven transmembrane segments indicative of a G protein coupled receptor (GPCR) superfamily. Significantly, reverse transcription polymerase chain reaction (RT-PCR) reveals that the tmt opsin genes in zebrafish are both temporally and spatially regulated. To investigate if these tmt photopigments mediate light-activated currents in cells, each opsin was expressed in vitro and the responses characterised by calcium imaging, whole-cell patch clamp electrophysiology, UV-Vis spectrophotometric analysis, and bioluminescence reporter assay. Collectively, these data suggest that some of the opsin photoproteins signal via Gi-type G protein pathway. Interestingly, the spectral analysis obtained shows that most tmt opsins tested are UV-sensitive when reconstituted in vitro with 11-cis and all-trans retinal, indicating an intrinsic bistable dynamics. Using site directed mutagenesis on one of the tmt opsins, tmt10, the potential spectral tuning sites involved in UV detection were tested. As part of this study, tmt opsin cDNAs were isolated from three populations of Mexican tetra (Astyanax mexicanus): surface, Pachon and Steinhardt. This allowed for a direct comparison between the tmt opsins present in the dark adapted species (cavefish) versus those of the light adapted species (zebrafish). It is hoped that the findings from this project will contribute to our understanding of non-visual light detection in fish and the evolution of their non-image forming photoreception.

Com o intuito de avaliar os polimorfismos de mtDNA e a diversidade genética na população brasileira, foram estudados 84 indivíduos não aparentados: 49 caucasóides e 35 negróides da região sudeste do Brasil. As amostras de sangue obtidas por punção da polpa digital foram colocadas em papel de filtro e o mtDNA extraído pelo método orgânico. Foram amplificadas as regiões hipervariáveis HV1 a partir do nucleotídeo 16.051 até 16.365 e HV2 entre os nucleotídeos 71 e 340. O fragmento foi purificado e após a reação de seqüenciamento, as fitas sense e anti-sense foram alinhadas com a seqüência de Anderson e sobrepostas para confirmação. Foram encontradas 108 posições contendo transições, 15 transversões, 11 deleções e 4 inserções. Nove regiões apresentaram duas variantes de seqüência polimórfica. A maioria das seqüências foi observada uma única vez e em 84 indivíduos foram observados 80 haplótipos distintos. O índice de diversidade genética e a probabilidade de semelhança entre duas seqüências escolhidas ao acaso foram respectivamente de 0,9714 e 0,0286 para os negróides e de 0,9788 e 0,0212 para os caucasóides. Ao realizar análise pareada dos haplótipos, a média de nucleotídeos diferentes entre as seqüências foi de 14,36 ± 5,68 bases em um total de 3.486 pares comparados, indicando uma alta diversidade entre haplótipos nesta população. Os resultados demonstraram que o mtDNA é informativo para identificação humana e o conhecimento da freqüência dos haplótipos na população de interesse tem utilidade significativa na aplicação Forense, principalmente para se avaliar estatisticamente os resultados, fornecendo maior precisão, exatidão e dados contundentes nas investigações.
In order to evaluate the mtDNA polymorphism and demonstrate the sequence diversity in Brazilians, we established a database of 84 unrelated individuals, 49 Caucasians and 35 negroids from the southeast of Brazil. The samples were collected on a whatman paper by finger punction, the mtDNA was extracted by organic method and hipervariable regions, HV1 from 16.051 to 16.365 bp and HV2 from 71 to 340 bp were amplified. Both sense and anti-sense strands were sequenced. When compared to Anderson sequence, 108 transitions, 15 transversions, 11 deletions and 4 insertions were found. Nine positions exhibited two variants of polymorphic sequence. The majority of the sequences were observed once, and in 84 sequences, 80 haplotypes were observed. The sequence diversity and the probability for two individuals randomly matching over two hypervariable regions were 0.9714 and 0.0286 for persons of color and 0.9788 and 0.0212 for Caucasians. In pair wise comparison, the mean sequence difference of 14,36 ± 5,68 nucleotides over 3,486 pairs compared, indicates a high diversity in this population. The data demonstrates that mtDNA sequencing can be informative in forensic cases, but it is of crucial importance to know the frequency of the mtDNA haplotypes to statistically evaluate the results.