Analysis of potential transcriptomic biomarkers for Huntington's disease in peripheral blood.

Highly quantitative biomarkers of neurodegenerative disease remain an important need in the urgent quest for disease-modifying therapies. For Huntington's disease (HD), a genetic test is available (trait marker), but necessary state markers are still in development. In this report, we describe a large battery of transcriptomic tests explored as state biomarker candidates. In an attempt to exploit the known neuroinflammatory and transcriptional perturbations of disease, we measured relevant mRNAs in peripheral blood cells. The performance of these potential markers was weak overall, with only one mRNA, immediate early response 3 (IER3), showing a modest but significant increase of 32% in HD samples compared with controls. No statistically significant differences were found for any other mRNAs tested, including a panel of 12 RNA biomarkers identified in a previous report [Borovecki F, Lovrecic L, Zhou J, Jeong H, Then F, Rosas HD, Hersch SM, Hogarth P, Bouzou B, Jensen RV, et al. (2005) Proc Natl Acad Sci USA 102:11023-11028]. The present results may nonetheless inform the future design and testing of HD biomarker strategies.

Analysis of gene expression patterns in animals

During my PhD, my aim was to provide new tools to increase our capacity to analyse gene expression patterns, and to study on a large-scale basis the evolution of gene expression in animals. Gene expression patterns (when and where a gene is expressed) are a key feature in understanding gene function, notably in development. It appears clear now that the evolution of developmental processes and of phenotypes is shaped both by evolution at the coding sequence level, and at the gene expression level.Studying gene expression evolution in animals, with complex expression patterns over tissues and developmental time, is still challenging. No tools are available to routinely compare expression patterns between different species, with precision, and on a large-scale basis. Studies on gene expression evolution are therefore performed only on small genes datasets, or using imprecise descriptions of expression patterns.The aim of my PhD was thus to develop and use novel bioinformatics resources, to study the evolution of gene expression. To this end, I developed the database Bgee (Base for Gene Expression Evolution). The approach of Bgee is to transform heterogeneous expression data (ESTs, microarrays, and in-situ hybridizations) into present/absent calls, and to annotate them to standard representations of anatomy and development of different species (anatomical ontologies). An extensive mapping between anatomies of species is then developed based on hypothesis of homology. These precise annotations to anatomies, and this extensive mapping between species, are the major assets of Bgee, and have required the involvement of many co-workers over the years. My main personal contribution is the development and the management of both the Bgee database and the web-application.Bgee is now on its ninth release, and includes an important gene expression dataset for 5 species (human, mouse, drosophila, zebrafish, Xenopus), with the most data from mouse, human and zebrafish. Using these three species, I have conducted an analysis of gene expression evolution after duplication in vertebrates.Gene duplication is thought to be a major source of novelty in evolution, and to participate to speciation. It has been suggested that the evolution of gene expression patterns might participate in the retention of duplicate genes. I performed a large-scale comparison of expression patterns of hundreds of duplicated genes to their singleton ortholog in an outgroup, including both small and large-scale duplicates, in three vertebrate species (human, mouse and zebrafish), and using highly accurate descriptions of expression patterns. My results showed unexpectedly high rates of de novo acquisition of expression domains after duplication (neofunctionalization), at least as high or higher than rates of partitioning of expression domains (subfunctionalization). I found differences in the evolution of expression of small- and large-scale duplicates, with small-scale duplicates more prone to neofunctionalization. Duplicates with neofunctionalization seemed to evolve under more relaxed selective pressure on the coding sequence. Finally, even with abundant and precise expression data, the majority fate I recovered was neither neo- nor subfunctionalization of expression domains, suggesting a major role for other mechanisms in duplicate gene retention.

Feasibility Study for Detection and Quantification of Corrosion in Bridge Barrier Rails, RB11-012, 2013

"Technical challenges exist with infrastructure that can be addressed by nondestructive evaluation (NDE) methods, such as detecting corrosion damage to reinforcing steel that anchor concrete bridge railings to bridge road decks. Moisture and chloride ions reach the anchors along the cold joint between the rails and deck, causing corrosion that weakens the anchors and ultimately the barriers. The Center for Nondestructive Evaluation at Iowa State University has experience in development of measurement techniques and new sensors using a variety of interrogating energies. This research evaluated feasibility of three technologies — x-ray radiation, ground-penetrating radar (GPR), and magnetic flux leakage (MFL) — for detection and quantification of corrosion of embedded reinforcing steel. Controlled samples containing pristine reinforcing steel with and without epoxy and reinforcing steel with 25 percent and 50 percent section reduction were embedded in concrete at 2.5 in. deep for laboratory evaluation. Two of the techniques, GPR and MFL, were used in a limited field test on the Iowa Highway 210 Bridge over Interstate 35 in Story County. The methods provide useful and complementary information. GPR provides a rapid approach to identify reinforcing steel that has anomalous responses. MFL provides similar detection responses but could be optimized to provide more quantitative correlation to actual condition. Full implementation could use either GPR or MFL methods to identify areas of concern, followed by radiography to give a visual image of the actual condition, providing the final guidance for maintenance actions." The full 103 page report and the 2 page Tech Transfer Summary are included in this link.

Anti-60-kDa heat shock protein antibodies in fetal serum: a biomarker for unexplained small for gestational age fetuses.

Introduction: Small for gestational age (SGA) is an important problem affecting 10% of pregnancies and is associated with significant perinatal morbidity. In about 80% of cases, a probable etiology or a major risk factor can be identified. But almost 20% of SGA cases are considered unexplained. The 60-kDa heat shock protein (HSP60) is a highly immunogenic protein whose synthesis is greatly upregulated under nonphysiological conditions. Bacterial and human HSP60 share a high degree of sequence homology, and immunity to conserved epitopes may result in development of autoimmunity following a bacterial infection. We hypothesized that unexplained SGA could be the consequence of immune sensitization to human HSP60. Methods: Unexplained SGA fetuses were identified by ultrasound biometry with normal Doppler velocimetry and with no detectable maternal or fetal abnormalities. Fetal sera were obtained by cordocentesis performed for a karyotype analysis in cases of unexplained SGA (study group) or for screening of Rhesus incompatibility (control group). Fetal sera were tested for HSP60 antigen and for IgG and IgM anti-HSP60 by ELISA as well as for other immune and hematological parameters. Results: Maternal parameters were similar between the 12 study cases and the 23 control cases. The mean gestational age at cordocentesis was 29 weeks. IgM anti-HSP60 was detected in 12 cases (100%) and in no controls (p < 0.00017), while IgG anti-HSP60 was detected in 7 cases (58%) and only 1 control (p < 0.001). Three of the 4 cases with the highest IgM antibody levels died. There were no differences in fetal serum levels of HSP60 antigen or other immune and hematological markers between the two groups. Conclusion: Fetuses with unexplained SGA are positive for IgM and IgG antibody to human HSP60 and the specific IgM antibody level is predictive of fetal mortality. Detection of these antibodies indicates that a placental perturbation and a fetal autoimmune reaction to HSP60 are associated with this developmental delay.

Catch-up growth strategies differ between body structures: interactions between age and structure-specific growth in wild nestling Alpine swifts

1. Little is known on the occurrence and magnitude of faster than normal (catch-up) growth in response to periods of undernutrition in the wild, and the extent to which different body structures compensate and over what timescales is poorly understood. 2. We investigated catch-up growth in nestling Alpine Swifts, Apus melba, by comparing nestling growth trajectories in response to a naturally occurring 1-week period of inclement weather and undernutrition with growth of nestlings reared in a good year. 3. In response to undernutrition, nestlings exhibited a hierarchy of tissues preservation and compensation, with body mass being restored quickly after the end of the period of undernutrition, acceleration of skeletal growth occurring later in development, and compensation in wing length occurring mostly due to a prolongation of growth and delayed fledging. 4. The effect of undernutrition and subsequent catch-up growth was age-dependent, with older nestlings being more resilient to undernutrition, and in turn having less need to compensate later in the development. 5. This shows that young in a free-living bird population can compensate in body mass and body size for a naturally occurring period of undernutrition, and that the timing and extent of compensation varies with age and between body structures.

Antagonistic effect of the inflammasome on thymic stromal lymphopoietin expression in the skin.

BACKGROUND: Innate immune sensors control key cytokines that regulate T-cell priming and T-cell fate. This is particularly evident in allergic reactions, which represent ideal systems to study the interplay of innate and adaptive immunity. In patients with contact dermatitis, inflammasome-mediated IL-1 activation is responsible for a TH1 immune response. Surprisingly, the IL-1 signaling pathway was also proposed to control the activation of thymic stromal lymphopoietin (TSLP), a cytokine implicated in development of the TH2 response in patients with atopic dermatitis (AD) and asthma. OBJECTIVES: We sought to assess the effect of the inflammasome on TSLP expression levels and the development of AD. METHODS: We studied the effect of the inflammasome activator 2,4-dinitrofluorobenzene, and IL-1β on TSLP mRNA expression levels in mouse and human cell lines (in vitro assays), as well as in live mice and on human skin transplants. We also assessed the effect of 2,4-dinitrofluorobenzene on TSLP and the TH2 response in mice in which the inflammasome and IL-1 signaling pathways were blocked, either genetically or pharmacologically, in 2 models of AD. RESULTS: We provide in vitro and in vivo evidence that inflammasome activation has an inhibitory role on TSLP mRNA expression and TH2 cell fate in the skin. We also show that solvents influence the activation of TSLP and IL-1β and direct the T-cell fate to a given hapten. CONCLUSION: Our observations strongly suggest that the TH1 versus TH2 cell fate decision is regulated at multiple levels and starts with innate immune events occurring within peripheral epithelial tissues.

Use of niche models in invasive species risk assessments.

Risk maps summarizing landscape suitability of novel areas for invading species can be valuable tools for preventing species' invasions or controlling their spread, but methods employed for development of such maps remain variable and unstandardized. We discuss several considerations in development of such models, including types of distributional information that should be used, the nature of explanatory variables that should be incorporated, and caveats regarding model testing and evaluation. We highlight that, in the case of invasive species, such distributional predictions should aim to derive the best hypothesis of the potential distribution of the species by using (1) all distributional information available, including information from both the native range and other invaded regions; (2) predictors linked as directly as is feasible to the physiological requirements of the species; and (3) modelling procedures that carefully avoid overfitting to the training data. Finally, model testing and evaluation should focus on well-predicted presences, and less on efficient prediction of absences; a k-fold regional cross-validation test is discussed.

Earliness per se and its dependence upon temperature in diploid wheat lines differing in the major gene Eps-Am1 alleles

Differences in development among wheat cultivars are not only restricted to photoperiod and vernalization responses. When both requirements are fully satisfied differences may still arise due to earliness per se. It is not clear at present to what extent this trait is ‘ intrinsically ’ expressed (a constitutive trait) independently of the environmental conditions so that it might be selected under any thermal condition or if it may be altered to the extent of showing a crossover interaction with temperature in which the ranking of wheat genotypes may be altered. The present study assessed the influence of temperature on the intrinsic earliness for lines of diploid wheat characterized for their differences in a major gene for intrinsic earliness, but also possibly differing in their genetic background for other factors controlling this polygenic trait. To do so the lines were grown individually in two temperature regimes (16 and 23 xC) under long days having previously been fully vernalized. Multiple comparisons analyses were carried out among lines of the same allelic group for the Eps-Am1 gene. Results indicated that within each group there were lines that did not differ in their earliness per se, others differed but without exhibiting any linertemperature interaction and finally different types of interaction were shown, including cases where the ranking of lines was altered depending on the growing temperature. It is thus possible that the selection of a genotype based on its earliness per se in an environment might not represent the same performance in another location where temperature varied significantly.

Sex-chromosome differentiation and 'sex races' in the common frog (Rana temporaria).

Sex-chromosome differentiation was recently shown to vary among common frog populations in Fennoscandia, suggesting a trend of increased differentiation with latitude. By rearing families from two contrasted populations (respectively, from northern and southern Sweden), we show this disparity to stem from differences in sex-determination mechanisms rather than in XY-recombination patterns. Offspring from the northern population display equal sex ratios at metamorphosis, with phenotypic sexes that correlate strongly with paternal LG2 haplotypes (the sex chromosome); accordingly, Y haplotypes are markedly differentiated, with male-specific alleles and depressed diversity testifying to their smaller effective population size. In the southern population, by contrast, a majority of juveniles present ovaries at metamorphosis; only later in development do sex ratios return to equilibrium. Even at these later stages, phenotypic sexes correlate only mildly with paternal LG2 haplotypes; accordingly, there are no recognizable Y haplotypes. These distinct patterns of gonadal development fit the concept of 'sex races' proposed in the 1930s, with our two populations assigned to the 'differentiated' and 'semi-differentiated' races, respectively. Our results support the suggestion that 'sex races' differ in the genetic versus epigenetic components of sex determination. Analysing populations from the 'undifferentiated race' with high-density genetic maps should help to further test this hypothesis.

Improving the effectiveness of supply chain development work – an expert role perspective

This study focuses to the intersection of three sets of activities in a company: expert work, development work and supply chain management, SCM. Experts and expert work represent a set of individuals whose efficiency and impact this study is intended to improve, while development work defines the set of organizational activities to focus on. SCM as an expertise area acts as the platform on which this study is built. The study has two aims. Firstly, it aims to derive a model helping an SCM expert to increase the effectiveness of expert work in development tasks by understanding the encountered organizational situations and processes better, reflecting his/her past and future actions to organizational processes and selecting and adjusting the processes and contents of his/her work accordingly. Secondly, it aims to develop applicable approaches and methods to understand, evaluate and manage the organizational processes and situations in development work. The integrative model on approaches and methods to improve the effectiveness of development processes is split to two aggregate dimensions: technical performance of the developed solution and consumption of resources of the development process. Six potential approaches and methods aiming at helping in the management of organizational dimensions are presented in enclosed publications. The approaches focus on three subtasks of development work: decision making, implementation and change, and knowledge accumulation. The approaches and methods have been tested in case studies representing typical development processes in the area of supply chain management. As a result, four suggestions are presented. Firstly, SCM experts are advised to consider the SCM development work to be consisting of development processes. Secondly, inside these processes they should identify and evaluate the risk of difficult decision-making related to organizational factors. Thirdly, they are prompted for an active role in implementation and change, supporting the implementation through whole process. Finally, the development should be seen in a holistic view, taking into account the stage of knowledge and organizational issues related to it, and adopt a knowledge development strategy.

Improving and User Interface to E-Procurement Software Used in Asset Accounting and Investigating Effects to Efficiency

This diploma thesis has been done to international organization which takes care from the accounting actions of two major companies. In this organization are used three different purchasing tools which are used when new asset master data is wanted to input to SAP R/3- system. The aim of this thesis is to find out how much changing the user interface of one of these three e-procurement programs will affect to overall efficiency in asset accounting. As an addition will be introduced project framework which can be used in future projects and which help to avoid certain steps in the development process. At the moment data needs to be inputted manually with many useless mouse clicks and data needs to be searched from many various resources which slow down the process. Other organization has better tools at the moment than the myOrders system which is under investigation Research was started by exploring the main improvement areas. After this possible defects were traced. Suggested improvements were thought by exploring literature which has been written from usability design and research. Meanwhile also directional calculations from the benefits of the project were done alongside with the analysis of the possible risks and threats. After this NSN IT approved the changes which they thought was acceptable. The next step was to program them into tool and test them before releasing to production environment. The calculations were made also from implemented improvements and compared them to planned ones From whole project was made a framework which can be utilized also to other similar projects. The complete calculation was not possible because of time schedule of the project. Important observation in the project was that efficiency is not improved not only by changing the GUI but also improving processes without any programming. Feedback from end user should be also listened more in development process. End-user is after all the one who knows the best how the program should look like.

Platform as a Service - new opportunities for software development companies

Today cloud computing is the next stage in development information-oriented society in field of information technologies. Great attention is paid to cloud computing in general, but the lack of scientific consideration to components brings to the problem, that not all aspects are well examined. This thesis is an attempt to consider Platform as a Service (a technology of providing development environment through the Internet) from divergent angles. Technical characteristics, costs, time, estimation of effectiveness, risks, strategies that can be applied, migration process, advantages and disadvantages and the future of the approach are examined to get the overall picture of cloud platforms. During the work literature study was used to examine Platform as a Service, characteristics of existent cloud platforms were explored and a model of a typical software development company was developed to create a scenario of migration to cloud technologies. The research showed that besides all virtues in reducing costs and time, cloud platforms have some significant obstacles in adoption. Privacy, security and insufficient legislation impede the concept to be widespread.

Genetic regulatory networks in avian B cells

Biology is turning into an information science. The science of systems biology seeks to understand the genetic networks that govern organism development and functions. In this study the chicken was used as a model organism in the study of B cell regulatory factors. These studies open new avenues for plasma cell research by connecting the down regulation of the B cell gene expression program directly to the initiation of plasma cell differentiation. The unique advantages of the DT40 avian B cell model system, specifically its high homologous recombination rate, were utilized to study gene regulation in Pax5 knock out cell lines and to gain new insights into the B cell to plasma cell transitions that underlie the secretion of antibodies as part of the adaptive immune response. The Pax5 transcription factor is central to the commitment, development and maintenance of the B cell phenotype. Mice lacking the Pax5 gene have an arrest in development at the pro-B lymphocyte stage while DT40 cells have been derived from cells at a more mature stage of development. The DT40 Pax5-/- cells exhibited gene expression similarities with primary chicken plasma cells. The expression of the plasma cell transcription factors Blimp-1 and XBP-1 were significantly upregulated while the expression of the germinal centre factor BCL6 was diminished in Pax5-/- cells, and this alteration was normalized by Pax5 re-introduction. The Pax5-deficient cells further manifested substantially elevated secretion of IgM into the supernatant, another characteristic of plasma cells. These results for the first time indicated that the downregulation of the Pax5 gene in B cells promotes plasma cell differentiation. Cross-species meta-analysis of chicken and mouse Pax5 gene knockout studies uncovers genes and pathways whose regulatory relationship to Pax5 has remained unchanged for over 300 million years. Restriction of the hematopoietic stem cell fate to produce T, B and NK cell lineages is dependent on the Ikaros and its molecular partners, the closely related Helios and Aiolos. Ikaros family members are zinc finger proteins which act as transcriptional repressors while helping to activate lymphoid genes. Helios in mice is expressed from the hematopoietic stem cell level onwards, although later in development its expression seems to predominate in the T cell lineage. This study establishes the emergence and sequence of the chicken Ikaros family members. Helios expression in the bursa of Fabricius, germinal centres and B cell lines suggested a role for Helios in the avian B-cell lineage, too. Phylogenetic studies of the Ikaros family connect the expansion of the Ikaros family, and thus possibly the emergence of the adaptive immune system, with the second round of genome duplications originally proposed by Ohno. Paralogs that have arisen as a result of genome-wide duplications are sometimes termed ohnologs – Ikaros family proteins appear to fit that definition. This study highlighted the opportunities afforded by the genome sequencing efforts and somatic cell reverse genetics approaches using the DT40 cell line. The DT40 cell line and the avian model system promise to remain a fruitful model for mechanistic insight in the post-genomic era as well.

Knowledge Sharing between Generations in an Organisation - Retention of the Old or Building the New?

The study explores knowledge transfer between retiring employees and their successors in expert work. My aim is to ascertain whether there is knowledge development or building new knowledge related to this organisational knowledge transfer between generations; in other words, is the transfer of knowledge from experienced, retiring employees to their successors merely retention of the existing organisational knowledge by distributing it from one individual to another or does this transfer lead to building new and meaningful organisational knowledge. I call knowledge transfer between generations and the possibly related knowledge building in this study knowledge sharing between generations. The study examines the organisation and knowledge management from a knowledge-based and constructionist view. From this standpoint, I see knowledge transfer as an interactive process, and the exploration is based on how the people involved in this process understand and experience the phenomenon studied. The research method is organisational ethnography. I conducted the analysis of data using thematic analysis and the articulation method, which has not been used before in organisational knowledge studies. The primary empirical data consists of theme interviews with twelve employees involved in knowledge transfer in the organisation being studied and five follow-up theme interviews. Six of the interviewees are expert duty employees due to retire shortly, and six are their successors. All those participating in the follow-up interviews are successors of those soon to retire from their expert responsibilities. The organisation in the study is a medium-sized Finnish firm, which designs and manufactures electrical equipment and systems for the global market. The results of the study show that expert work-related knowledge transfer between generations can mean knowledge building which produces new, meaningful knowledge for the organisation. This knowledge is distributed in the organisation to all those that find it useful in increasing the efficiency and competitiveness of the whole organisation. The transfer and building of knowledge together create an act of knowledge sharing between generations where the building of knowledge presupposes transfer. Knowledge sharing proceeds between the expert and the novice through eight phases. During the phases of knowledge transfer the expert guides the novice to absorb the knowledge to be transferred. With the expert’s help the novice gradually comes to understand the knowledge and in the end he or she is capable of using it in his or her work. During the phases of knowledge building the expert helps the novice to further develop the knowledge being transferred so that it becomes new, useful knowledge for the organisation. After that the novice takes the built knowledge to use in his or her work. Based on the results of the study, knowledge sharing between generations takes place in interaction and ends when knowledge is taken to use. The results I obtained in the interviews by the articulation method show that knowledge sharing between generations is shaped by the novices’ conceptions of their own work goals, knowledge needs and duties. These are not only based on the official definition of the work, but also how the novices find their work or how they prioritise the given objectives and responsibilities. The study shows that the novices see their work primarily as maintenance or development. Those primarily involved in maintenance duties do not necessarily need knowledge defined as transferred between generations. Therefore, they do not necessarily transfer knowledge with their assigned experts, even though this can happen in favourable circumstances. They do not build knowledge because their view of their work goals and duties does not require the building of new knowledge. Those primarily involved in development duties, however, do need knowledge available from their assigned experts. Therefore, regardless of circumstances they transfer knowledge with their assigned experts and also build knowledge because their work goals and duties create a basis for building new knowledge. The literature on knowledge transfer between generations has focused on describing either the knowledge being transferred or the means by which it is transferred. Based on the results of this study, however, knowledge sharing between generations, that is, transfer and building is determined by how the novice considers his or her own knowledge needs and work practices. This is why studies on knowledge sharing between generations and its implementation should be based not only on the knowledge content and how it is shared, but also on the context of the work in which the novice interprets and shares knowledge. The existing literature has not considered the possibility that knowledge transfer between generations may mean building knowledge. The results of this study, however, show that this is possible. In knowledge building, the expert’s existing organisational knowledge is combined with the new knowledge that the novice brings to the organisation. In their interaction this combination of the expert’s “old” and the novice’s “new” knowledge becomes new, meaningful organisational knowledge. Previous studies show that knowledge development between the members of an organisation is the prerequisite for organisational renewal which in turn is essential for improved competitiveness. Against this background, knowledge building enables organisational renewal and thus enhances competitiveness. Hence, when knowledge transfer between generations is followed by knowledge building, the organisation kills two birds with one stone. In knowledge transfer the organisation retains the existing knowledge and thus maintains its competitiveness. In knowledge building the organisation developsnew knowledge and thus improves its competitiveness.

Use of preclinical and early clinical data for dose selection of a selective estrogen receptor modulator toremifene in treatment of breast cancer

In development of human medicines, it is important to predict early and accurately enough the disease and patient population to be treated as well as the effective and safe dose range of the studied medicine. This is pursued by using preclinical research models, clinical pharmacology and early clinical studies with small sample sizes. When successful, this enables effective development of medicines and reduces unnecessary exposure of healthy subjects and patients to ineffectice or harmfull doses of experimental compounds. Toremifene is a selective estrogen receptor modulator (SERM) used for treatment of breast cancer. Its development was initiated in 1980s when selection of treatment indications and doses were based on research in cell and animal models and on noncomparative clinical studies including small number of patients. Since the early development phase, the treatment indication, the patient population and the dose range were confirmed in large comparative clinical studies in patients. Based on the currently available large and long term clinical study data the aim of this study was to investigate how the early phase studies were able to predict the treatment indication, patient population and the dose range of the SERM. As a conclusion and based on the estrogen receptor mediated mechanism of action early studies were able to predict the treatment indication, target patient population and a dose range to be studied in confirmatory clinical studies. However, comparative clinical studies are needed to optimize dose selection of the SERM in treatment of breast cancer.