Molecular Characteristics of Neuroblastoma with Special Reference to Novel Prognostic Factors and Diagnostic Applications

Molecular Characteristics of Neuroblastoma with Special Reference to Novel Prognostic Factors and Diagnostic Applications Department of Medical Biochemistry and Genetics Annales Universitatis Turkuensis, Medica-Odontologica, 2009, Turku, Finland Painosalama Oy, Turku, Finland 2009 Background: Neuroblastoma, which is the most common and extensively studied childhood solid cancer, shows a great clinical and biological heterogeneity. Most of the neuroblastoma patients older than one year have poor prognosis despite intensive therapies. The hallmark of neuroblastoma, biological heterogeneity, has hindered the discovery of prognostic tumour markers. At present, few molecular markers, such as MYCN oncogene status, have been adopted into clinical practice. Aims: The aim of the study was to improve the current prognostic methodology of neuroblastoma, especially by taking cognizance of the biological heterogeneity of neuroblastoma. Furthermore, unravelling novel molecular characteristics which associate with neuroblastoma tumour progression and cell differentiation was an additional objective. Results: A new strictly defined selection of neuroblastoma tumour spots of highest proliferation activity, hotspots, appeared to be representative and reliable in an analysis of MYCN amplification status using a chromogenic in situ hybridization technique (CISH). Based on the hotspot tumour tissue microarray immunohistochemistry and high-resolution oligo-array-based comparative genomic hybridization, which was integrated with gene expression and in silico analysis of existing transcriptomics, a polysialylated neural cell adhesion molecule (NCAM) and poorly characterized amplicon at 12q24.31 were discovered to associate with outcome. In addition, we found that a previously considered new neuroblastoma treatment target, the mutated c-kit receptor, was not mutated in neuroblastoma samples. Conclusions: Our studies indicate polysialylated NCAM and 12q24.31 amplicon to be new molecular markers with important value in prognostic evaluation of neuroblastoma. Moreover, the presented hotspot tumour tissue microarray method together with the CISH technique of the MYCN oncogene copy number is directly applicable to clinical use. Key words: neuroblastoma, polysialic acid, neural cell adhesion molecule, MYCN, c-kit, chromogenic in situ hybridization, hotspot

Molecular profiling of human endometrium and endometriosis

Endometriosis is a common hormone-dependent gynecological disease leading to severe menstrual and/or chronic pelvic pain with or without subfertility. The disease is defined by the presence of endometrium-like tissue outside the uterine cavity, primarily on the pelvic peritoneum, ovaries and infiltrating organs of the peritoneal cavity. The current tools for diagnosis and treatment of endometriosis need to be improved to ensure reliable diagnosis and effective treatment. In addition, endometriosis is associated with increased risk of ovarian cancer and, therefore, the differential diagnosis between the benign and malignant ovarian cysts is of importance. The long-term objective of the present study was to support the discovery of novel tools for diagnosis and treatment of endometriosis. This was approached by exploiting genome-wide expression analysis of endometriosis specimens. A novel expression profiling -based classification of endometriosis indicated specific subgroups of lesions partially consistent with the clinical appearance, but partially according to unknown factors. The peritoneum of women with endometriosis appeared to be altered in comparison to that of healthy control subjects, suggesting a novel aspect on the pathogenesis of the disease. The evaluation of action and metabolism of sex hormones in endometrium and endometriosis tissue indicated a novel role of androgens in regulation of the tissues. In addition, an enzyme involved in androgen and neurosteroid metabolism, hydroxysteroid (17beta) dehydrogenase 6, was found to be highly up-regulated in endometriosis tissue as compared to healthy endometrium. The enzyme may have a role in the pathogenesis of endometriosis or in the endometriosis associated pain generation. Finally, a new diagnostic biomarker, HE4, was discovered distinguishing patients with ovarian endometriotic cysts from those with malignant ovarian cancer. The information acquired in this study enables deeper understanding of endometriosis and facilitates the development of improved diagnostic tools and more specific treatments of the disease

Effects of interband and intraband impurity scattering on coherence length in the pnictide superconductors

After discovery of cuprates, a search for new high temperature superconducting families began and it led to the discovery of layered pnictide compounds with critical temperatures limited up to ∼56 K. Pnictides consist elements from Group V of Periodic Table (nitrogen, phosphorus, arsenic, antimony and bismuth). In this work coherence length h in mixed state of pnictide superconductors is calculated numerically. In calculation is taken into account interband and intraband impurity scattering in framework of quasiclassical Eilenberger theory for s± pairing symmetry. Differences between Ginzburg-Landau and Eilenberger theories is shown and the comparison with existing models is done.

Effects of interband and intraband impurity scattering on coherence length in the pnictide superconductors

After discovery of cuprates, a search for new high temperature superconducting families began and it led to the discovery of layered pnictide compounds with critical temperatures limited up to ~56 K. Pnictides consist elements from Group V of Periodic Table (nitrogen, phosphorus, arsenic, antimony and bismuth). In this work coherence length ξh in mixed state of pnictide superconductors is calculated numerically. In calculation is taken into account interband and intraband impurity scattering in framework of quasiclassical Eilenberger theory for s± pairing symmetry. Differences between Ginzburg-Landau and Eilenberger theories is shown and the comparison with existing models is done.

The spindle assembly checkpoint as a drug target - Novel small-molecule inhibitors of Aurora kinases

Cell division (mitosis) is a fundamental process in the life cycle of a cell. Equal distribution of chromosomes between the daughter cells is essential for the viability and well-being of an organism: loss of fidelity of cell division is a contributing factor in human cancer and also gives rise to miscarriages and genetic birth defects. For maintaining the proper chromosome number, a cell must carefully monitor cell division in order to detect and correct mistakes before they are translated into chromosomal imbalance. For this purpose an evolutionarily conserved mechanism termed the spindle assembly checkpoint (SAC) has evolved. The SAC comprises a complex network of proteins that relay and amplify mitosis-regulating signals created by assemblages called kinetochores (KTs). Importantly, minor defects in SAC signaling can cause loss or gain of individual chromosomes (aneuploidy) which promotes tumorigenesis while complete failure of SAC results in cell death. The latter event has raised interest in discovery of low molecular weight (LMW) compounds targeting the SAC that could be developed into new anti-cancer therapeutics. In this study, we performed a cell-based, phenotypic high-throughput screen (HTS) to identify novel LMW compounds that inhibit SAC function and result in loss of cancer cell viability. Altogether, we screened 65 000 compounds and identified eight that forced the cells prematurely out of mitosis. The flavonoids fisetin and eupatorin, as well as the synthetic compounds termed SACi2 and SACi4, were characterized in more detail utilizing versatile cell-based and biochemical assays. To identify the molecular targets of these SAC-suppressing compounds, we investigated the conditions in which SAC activity became abrogated. Eupatorin, SACi2 and SACi4 preferentially abolished the tensionsensitive arm of the SAC, whereas fisetin lowered also the SAC activity evoked by lack of attachments between microtubules (MTs) and KTs. Consistent with the abrogation of SAC in response to low tension, our data indicate that all four compounds inhibited the activity of Aurora B kinase. This essential mitotic protein is required for correction of erratic MT-KT attachments, normal SAC signaling and execution of cytokinesis. Furthermore, eupatorin, SACi2 and SACi4 also inhibited Aurora A kinase that controls the centrosome maturation and separation and formation of the mitotic spindle apparatus. In line with the established profound mitotic roles of Aurora kinases, these small compounds perturbed SAC function, caused spindle abnormalities, such as multi- and monopolarity and fragmentation of centrosomes, and resulted in polyploidy due to defects in cytokinesis. Moreover, the compounds dramatically reduced viability of cancer cells. Taken together, using a cell-based HTS we were able to identify new LMW compounds targeting the SAC. We demonstrated for the first time a novel function for flavonoids as cellular inhibitors of Aurora kinases. Collectively, our data support the concept that loss of mitotic fidelity due to a non-functional SAC can reduce the viability of cancer cells, a phenomenon that may possess therapeutic value and fuel development of new anti-cancer drugs.

Circular Spectropolarimetric Studies of DQ White Dwarfs

This thesis summarizes studies of a class of white dwarfs (WDs) called DQ WDs. White dwarfs are the remnants of ordinary stars like our Sun that have run out of nuclear fuel. WDs are classified according to the composition of their atmosphere and DQ WDs have an atmosphere made of helium and carbon. The carbon comes in either atomic or molecular form and in some cases the strong spectral absorption features cover the entire optical wavelength region. The research presented here utilizes spectropolarimetry, which is an observational technique that combines spectroscopy and polarization. Separately these allow to study the composition of a target and the inhomogeneous distribution of matter in the target. Put together they form a powerful tool to probe the physical properties in the atmosphere of a star. It is espacially good for detecting magnetic fields. The papers in this thesis describe efforts to do a survey of DQ white dwarfs with spectropolarimetry in order to search for magnetic fields in them. Paper I describes the discovery of a new magnetic cool DQ white dwarf, GJ841B. Initial modeling of molecular features on DQ WDs showed inconsistencies with observations. The first possible solution to this problem was stellar spots on these WDs. To investigate the matter, two DQ WDs were monitored for photometric variability that could arise from the presence of such spots. Paper II summarizes this short campaign and reports the negative results. Paper III reports observations of the rest of the objects in our survey. The paper includes the discovery of polarization from another cool DQ white dwarf, bringing the total of known magnetic cool DQs to three. Unfortunately the model used in this thesis cannot, in its present state, be used to model these objects nor are the observations of high enough spectroscopic resolution to do so.

Aqueous-phase reforming of renewables for selective hydrogen production in the presence of supported platinum catalysts

The evolution of our society is impossible without a constant progress in life-important areas such as chemical engineering and technology. Innovation, creativity and technology are three main components driving the progress of chemistry further towards a sustainable society. Biomass, being an attractive renewable feedstock for production of fine chemicals, energy-rich materials and even transportation fuels, captures progressively new positions in the area of chemical technology. Knowledge of heterogeneous catalysis and chemical technology applied to transformation of biomass-derived substances will open doors for a sustainable economy and facilitates the discovery of novel environmentally-benign processes which probably will replace existing technologies in the era of biorefinary. Aqueous-phase reforming (APR) is regarded as a promising technology for production of hydrogen and liquids fuels from biomass-derived substances such as C3-C6 polyols. In the present work, aqueous-phase reforming of glycerol, xylitol and sorbitol was investigated in the presence of supported Pt catalysts. The catalysts were deposited on different support materials, including Al2O3, TiO2 and carbons. Catalytic measurements were performed in a laboratory-scale continuous fixedbed reactor. An advanced analytical approach was developed in order to identify reaction products and reaction intermediates in the APR of polyols. The influence of the substrate structure on the product formation and selectivity in the APR reaction was also investigated, showing that the yields of the desired products varied depending on the substrate chain length. Additionally, the influence of bioethanol additive in the APR of glycerol and sorbitol was studied. A reaction network was advanced explaining the formation of products and key intermediates. The structure sensitivity in the aqueous-phase reforming reaction was demonstrated using a series of platinum catalysts supported on carbon with different Pt cluster sizes in the continuous fixed-bed reactor. Furthermore, a correlation between texture physico-chemical properties of the catalysts and catalytic data was established. The effect of the second metal (Re, Cu) addition to Pt catalysts was investigated in the APR of xylitol showing a superior hydrocarbon formation on PtRe bimetallic catalysts compared to monometallic Pt. On the basis of the experimental data obtained, mathematical modeling of the reaction kinetics was performed. The developed model was proven to successfully describe experimental data on APR of sorbitol with good accuracy.

Envia – a repository for environmental information access and discovery

Poster at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

The early activities of front end of innovation in oem companies using a new fei platform as a framework for renewal

The main goal of this study is to create a seamless chain of actions and more detailed structure to the front end of innovation to be able to increase the front end performance and finally to influence the renewal of companies. The main goal is achieved through by the new concept of an integrated model of early activities of FEI leading to a discovery of new elements of opportunities and the identification of new business and growth areas. The procedure offers one possible solution to a dynamic strategy formation process in innovation development cycle. In this study the front end of innovation is positioned between a strategy reviews and a concept creation with needed procedures, tools, and frameworks. The starting point of the study is that the origins of innovation are not well enough understood. The study focuses attention on the early activities of FEI. These first activities are conceptualized in order to find out successful innovation initiatives and strategic renewal agendas. A seamless chain of activities resulting in faster and more precise identification of opportunities and growth areas available on markets and inside companies is needed. Three case studies were conducted in order to study company views on available theory doctrine and to identify the first practical experiences and procedures in the beginning of the front end of innovation. Successful innovation requires focus on renewal in both internal and external directions and they should be carefully balanced for best results. Instead of inside-out mode of actions the studied companies have a strong outside-in thinking mode and they mainly co-develop their innovation initiatives in close proximity with customers i.e. successful companies are an integral part of customers business and success. Companies have tailor-made innovation processes combined their way of working linked to their business goals, and priorities of actual needs of transformation. The result of this study is a new modular FEI platform which can be configured by companies against their actual business needs and drivers. This platform includes new elements of FEI documenting an architecture presenting how the system components work together. The system is a conceptual approach from theories of emergent strategy formation, opportunity identification and creation, interpretation-analysis-experimentation triad and the present FEI theories. The platform includes new features compared to actual models of FEI. It allows managers to better understand the importance of FEI in the whole innovation development stage and FEI as a phase and procedure to discover and implement emergent strategy. An adaptable company rethinks and redirects strategy proactively from time to time. Different parts of the business model are changed to remove identified obstacles for growth and renewal which gives them avenues to find right reforms for renewal.

New methods for controlling twin configurations and characterizing twin boundaries in 5M Ni-Mn-Ga for the development of applications

Traditional methods for studying the magnetic shape memory (MSM) alloys Ni-Mn-Ga include subjecting the entire sample to a uniform magnetic field or completely actuating the sample mechanically. These methods have produced significant results in characterizing the MSM effect, the properties of Ni-Mn-Ga and have pioneered the development of applications from this material. Twin boundaries and their configuration within a Ni-Mn-Ga sample are a key component in the magnetic shape memory effect. Applications that are developed require an understanding of twin boundary characteristics and, more importantly, the ability to predictably control them. Twins have such a critical role that the twinning stress of a Ni-Mn-Ga crystal is the defining characteristic that indicates its quality and significant research has been conducted to minimize this property. This dissertation reports a decrease in the twinning stress, predictably controlling the twin configuration and characterizing the dynamics of twin boundaries. A reduction of the twinning stress is demonstrated by the discovery of Type II twins within Ni-Mn-Ga which have as little as 10% of the twinning stress of traditional Type I twins. Furthermore, new methods of actuating a Ni-Mn-Ga element using localized unidirectional or bidirectional magnetic fields were developed that can predictably control the twin configuration in a localized area of a Ni-Mn-Ga element. This method of controlling the local twin configuration was used in the characterization of twin boundary dynamics. Using a localized magnetic pulse, the velocity and acceleration of a single twin boundary were measured to be 82.5 m/s and 2.9 × 107 m/s2, and the time needed for the twin boundary to nucleate and begin moving was less than 2.8 μs. Using a bidirectional magnetic field from a diametrically magnetized cylindrical magnet, a highly reproducible and controllable local twin configuration was created in a Ni-Mn-Ga element which is the fundamental pumping mechanism in the MSM micropump that has been co-invented and extensively characterized by the author.

Synthesis of Short Oligonucleotides on a Soluble Support by the Phosphoramidite Method

In the last decades, the chemical synthesis of short oligonucleotides has become an important aspect of study due to the discovery of new functions for nucleic acids such as antisense oligonucleotides (ASOs), aptamers, DNAzymes, microRNA (miRNA) and small interfering RNA (siRNA). The applications in modern therapies and fundamental medicine on the treatment of different cancer diseases, viral infections and genetic disorders has established the necessity to develop scalable methods for their cheaper and easier industrial manufacture. While small scale solid-phase oligonucleotide synthesis is the method of choice in the field, various challenges still remain associated with the production of short DNA and RNA-oligomers in very large quantities. On the other hand, solution phase synthesis of oligonucleotides offers a more predictable scaling-up of the synthesis and is amenable to standard industrial manufacture techniques. In the present thesis, various protocols for the synthesis of short DNA and RNA oligomers have been studied on a peracetylated and methylated β-cyclodextrin, and also on a pentaerythritol-derived support. On using the peracetylated and methylated β-cyclodextrin soluble supports, the coupling cycle was simplified by replacement of the typical 5′-O-(4,4′-dimethoxytrityl) protecting group with an acid-labile acetal-protected 5′-O-(1-methoxy-1-methylethyl) group, which upon acid-catalyzed methanolysis released easily removable volatile products. For this reason monomeric building blocks 5′-O-(1-methoxy-1-methylethyl) 3′-(2-cyano-ethyl-N,N-diisopropylphosphoramidite) were synthesized. Alternatively, on using the precipitative pentaerythritol support, novel 2´-O-(2-cyanoethyl)-5´-O-(1-methoxy-1-methylethyl) protected phosphoramidite building blocks for RNA synthesis have been prepared and their applicability by the synthesis of a pentamer was demonstrated. Similarly, a method for the preparation of short RNAs from commercially available 5´-O-(4,4´-dimethoxytrityl)-2´-O-(tert-butyldimethyl-silyl)ribonucleoside 3´-(2-cyanoethyl-N,N-diisopropylphosphoramidite) building blocks has been developed