Lipid-Containing Icosahedral dsDNA Bacteriophages: Entry, Exit and Structure

In this thesis three icosahedral lipid-containing double-stranded (ds) deoxyribonucleic acid (DNA) bacteriophages have been studied: PRD1, Bam35 and P23-77. The work focuses on the entry, exit and structure of the viruses. PRD1 is the type member of the Tectiviridae family, infecting a variety of Gram-negative bacteria. The PRD1 receptor binding complex, consisting of the penton protein P31, the spike protein P5 and the receptor binding protein P2 recognizes a specific receptor on the host surface. In this study we found that the transmembrane protein P16 has an important stabilization function as the fourth member of the receptor binding complex and protein P16 may have a role in the formation of a tubular membrane structure, which is needed in the ejection of the genome into the cell. Phage Bam35 (Tectiviridae), which infects Gram-positive hosts, has been earlier found to resemble PRD1 in morphology and genome organization The uncharacterized early and late events in the Bam35 life cycle were studied by electrochemical methods. Physiological changes in the beginning of the infection were found to be similar in both lysogenic and nonlysogenic cell lines, Bam35 inducing a temporal decrease of membrane voltage and K+ efflux. At the end of the infection cycle physiological changes were observed only in the nonlysogenic cell line. The strong K+ efflux 40 min after infection and the induced premature cell lysis propose that Bam35 has a similar holin-endolysin lysis system to that of PRD1. Thermophilic icosahedral dsDNA Thermus phages P23-65H, P23-72 and P23-77 have been proposed to belong to the Tectiviridae family. In this study these phages were compared to each other. Analysis of structural protein patterns and stability revealed these phages to be very similar but not identical. The most stable of the studied viruses, P23-77, was further analyzed in more detail. Cryo-electron microscopy and three-dimensional image reconstruction was used to determine the structure of virus to 14 Å resolution. Results of thin layer chromatography for neutral lipids together with analysis of the three dimensional reconstruction of P23-77 virus particle revealed the presence of an internal lipid membrane. The overall capsid architecture of P23-77 is similar to PRD1 and Bam35, but most closely it resembles the structure of the capsid of archaeal virus SH1. This complicates the classification of dsDNA, internal lipid-containing icosahedral viruses.

The family Herbertaceae and its novel systematic position within liverworts

Taxonomic relationships of the liverwort genus Herbertus in Asia were examined. In addition, the phylogeny of the family Herbertaceae and its close relatives was investigated and analyses conducted of higher level relationships within the entire liverwort phylum. Species of Herbertus show great plasticity in various morphological characters, resulted in a large number of described species. This study was the first comprehensive revision of Asian Herbertus, with 12 species recognized for the continent. Eleven names were reduced to synonymy under earlier described species, and one species was excluded from the genus. Herbertus buchii Juslén was described as a new species. Phylogenetic analyses based on both molecular and morphological characters resolved the families Vetaformaceae, Lepicoleaceae, and Herbertaceae (including Mastigophoraceae) as a monophyletic entity. This clade is among the most derived groups within the leafy liverworts and comprises mostly isophyllous plants, all of which have bracteolar antheridia. The relationships of Mastigophoraceae have formerly been controversial. My results confirm the view that this family is closely related to Herbertaceae, Lepicoleaceae, and Vetaformaceae. In the proposed new classification Mastigophoraceae is included in Herbertaceae. Phylogenetic relationships within the liverworts were reconstructed using both chloroplast and nuclear sequences as well as morphological characters. These analyses were the most comprehensive to date at the time of publication. Previously it was believed that liverworts had a common ancestor with an erect, radial gametophyte and a tetrahedral apical cell. The leafy liverworts were arranged based on the assumption that similar structures had repeatedly developed in many different suborders, with evolution proceeding from erect and isophyllous to creeping and anisophyllous plants. The complex thalloid liverworts were assumed to be the most derived group. By contrast, our studies resolved a clade comprising Treubia and Haplomitrium as the earliest extant liverwort lineage. According to our results the complex thalloids are also an early diverging lineage, and the simple thalloids, traditionally classified together, are a paraphyletic group. Within leafy liverworts, the hypothesis of repeated evolution from isophyllous to anisophyllous plants based on the assumption of a basal unresolved polytomy was rejected. Fundamentally, the leafy liverworts can be divided into three groups. In conflict with the earlier hypotheses, the isophyllous liverworts, including Herbertaceae, were resolved as derived lineages within the liverworts.

Genetic analysis of chromosomal regions 2q33, 7q32 and 19q13 in multiple sclerosis susceptibility

Multiple sclerosis (MS) is an immune-mediated demyelinating disorder of the central nervous system (CNS) affecting 0.1-0.2% of Northern European descent population. MS is considered to be a multifactorial disease, both environment and genetics play a role in its pathogenesis. Despite several decades of intense research, the etiological and pathogenic mechanisms underlying MS remain still largely unknown and no curative treatment exists. The genetic architecture underlying MS is complex with multiple genes involved. The strongest and the best characterized predisposing genetic factors for MS are located, as in other immune-mediated diseases, in the major histocompatibility complex (MHC) on chromosome 6. In humans MHC is called human leukocyte antigen (HLA). Alleles of the HLA locus have been found to associate strongly with MS and remained for many years the only consistently replicable genetic associations. However, recently other genes located outside the MHC region have been proposed as strong candidates for susceptibility to MS in several studies. In this thesis a new genetic locus located on chromosome 7q32, interferon regulatory factor 5 (IRF5), was identified in the susceptibility to MS. In particular, we found that common variation of the gene was associated with the disease in three different populations, Spanish, Swedish and Finnish. We also suggested a possible functional role for one of the risk alleles with impact on the expression of the IRF5 locus. Previous studies have pointed out a possible role played by chromosome 2q33 in the susceptibility to MS and other autoimmune disorders. The work described here also investigated the involvement of this chromosomal region in MS predisposition. After the detection of genetic association with 2q33 (article-1), we extended our analysis through fine-scale single nucleotide polymorphism (SNP) mapping to define further the contribution of this genomic area to disease pathogenesis (article-4). We found a trend (p=0.04) for association to MS with an intronic SNP located in the inducible T-cell co-stimulator (ICOS) gene, an important player in the co-stimulatory pathway of the immune system. Expression analysis of ICOS revealed a novel, previously uncharacterized, alternatively spliced isoform, lacking the extracellular domain that is needed for ligand binding. The stability of the newly-identified transcript variant and its subcellular localization were analyzed. These studies indicated that the novel isoform is stable and shows different subcellular localization as compared to full-length ICOS. The novel isoform might have a regulatory function, but further studies are required to elucidate its function. Chromosome 19q13 has been previously suggested as one of the genomic areas involved in MS predisposition. In several populations, suggestive linkage signals between MS predisposition and 19q13 have been obtained. Here, we analysed the role of allelic variation in 19q13 by family based association analysis in 782 MS families collected from Finland. In this dataset, we were not able to detect any statistically significant associations, although several previously suggested markers were included to the analysis. Replication of the previous findings on the basis of linkage disequilibrium between marker allele and disease/risk allele appears notoriously difficult because of limitations such as allelic heterogeneity. Re-sequencing based approaches may be required for elucidating the role of chromosome 19q13 with MS. This thesis has resulted in the identification of a new MS susceptibility locus (IRF5) previously associated with other inflammatory or autoimmune disorders, such as SLE. IRF5 is one of the mediators of interferons biological function. In addition to providing new insight in the possible pathogenetic pathway of the disease, this finding suggests that there might be common mechanisms between different immune-mediated disorders. Furthermore the work presented here has uncovered a novel isoform of ICOS, which may play a role in regulatory mechanisms of ICOS, an important mediator of lymphocyte activation. Further work is required to uncover its functions and possible involvement of the ICOS locus in MS susceptibility.

Generalizations and Models in Ecology : Lawlikeness, Invariance, Stability, and Robustness

The question at issue in this dissertation is the epistemic role played by ecological generalizations and models. I investigate and analyze such properties of generalizations as lawlikeness, invariance, and stability, and I ask which of these properties are relevant in the context of scientific explanations. I will claim that there are generalizable and reliable causal explanations in ecology by generalizations, which are invariant and stable. An invariant generalization continues to hold or be valid under a special change called an intervention that changes the value of its variables. Whether a generalization remains invariant during its interventions is the criterion that determines whether it is explanatory. A generalization can be invariant and explanatory regardless of its lawlike status. Stability deals with a generality that has to do with holding of a generalization in possible background conditions. The more stable a generalization, the less dependent it is on background conditions to remain true. Although it is invariance rather than stability of generalizations that furnishes us with explanatory generalizations, there is an important function that stability has in this context of explanations, namely, stability furnishes us with extrapolability and reliability of scientific explanations. I also discuss non-empirical investigations of models that I call robustness and sensitivity analyses. I call sensitivity analyses investigations in which one model is studied with regard to its stability conditions by making changes and variations to the values of the model s parameters. As a general definition of robustness analyses I propose investigations of variations in modeling assumptions of different models of the same phenomenon in which the focus is on whether they produce similar or convergent results or not. Robustness and sensitivity analyses are powerful tools for studying the conditions and assumptions where models break down and they are especially powerful in pointing out reasons as to why they do this. They show which conditions or assumptions the results of models depend on. Key words: ecology, generalizations, invariance, lawlikeness, philosophy of science, robustness, explanation, models, stability

Transfers of Family Businesses to Non-Family Buyers - The Selling Business Family Perspective

This study focuses on business families and how they handle transitions such as business transfers. It also tries to shift the balance of research away from successions and towards business transfers as a key topic for family business researchers. In addition, it contributes to the family business research field by further highlighting the importance of the various different contributions in the family business from business family members other than the entrepreneurial founder. Based on interviews with both business family members and business brokers, it appears as important for business families who are selling their family business that it is managed in a similar way in the future regardless of the shift in ownership and management. It is also important that the employees can stay with the business. However, employees are seldom regarded as potential buyers of the family business; most preferably, from the point of view of business family members, this should be somebody who is similar to themselves. Business transfers can be lengthy processes, but once the family business is sold, previous owners most often want to leave the family business. This disengagement can be difficult for business family members if they have not managed to build up some other identity outside the family business environment. Money may compensate for the loss in the short run, but something else is needed in the long run, since the management of money is usually not perceived as that interesting. A family business transfer can have great influence on the members of the business family who is selling, and therefore it is suggested that personal due diligence could be of some help when planning the transfer. That tool can help business family members to analyse their own personal situation, but it may also make it easier to understand how the other business family members feel about the forthcoming change. Everyone is influenced in different ways during a family business transfer, and awareness of this fact may make it easier for the whole business family to adjust to their new environment.

Constructing Stability in Software Product Development during Organizational Restructurings

We all have fresh in our memory what happened to the IT sector only a few years ago when the IT-bubble burst. The upswing of productivity in this sector slowed down, investors lost large investments, many found themselves looking for a new job, and countless dreams fell apart. Product developers in the IT sector have experienced a large number of organizational restructurings since the IT boom, including rapid growth, downsizing processes, and structural reforms. Organizational restructurings seem to be a complex and continuous phenomenon people in this sector have to deal with. How do software product developers retrospectively construct their work in relation to organizational restructurings? How do organizational restructurings bring about specific social processes in product development? This working paper focuses on these questions. The overall aim is to develop an understanding of how software product developers construct their work during organizational restructurings. The theoretical frame of reference is based on a social constructionist approach and discourse analysis. This approach offers more or less radical and critical alternatives to mainstream organizational theory. Writings from this perspective attempt to investigate and understand sociocultural processes by which various realities are created. Therefore these studies aim at showing how people participate in constituting the social world (Gergen & Thatchenkery, 1996); knowledge of the world is seen to be constructed between people in daily interaction, in which language plays a central role. This means that interaction, especially the ways of talking and writing about product development during organizational restructurings, become the target of concern. This study consists of 25 in-depth interviews following a pilot study based on 57 semi-structured interviews. In this working paper I analyze 9 in-depth interviews. The interviews were conducted in eight IT firms. The analysis explores how discourses are constructed and function, as well as the consequences that follow from different discourses. The analysis shows that even though the product developers have experienced many organizational restructurings, some of which have been far-reaching, their accounts build strongly on a stability discourse. According to this discourse product development is, perhaps surprisingly, not influenced to a great extent by organizational restructurings. This does not mean that product development is static. According to the social constructionist approach, product development is constantly being reproduced and maintained in ongoing processes. In other words stable effects are also ongoing achievements and these are of particular interest in this study. The product developers maintain rather than change the product development through ongoing processes of construction, even when they experience continuous extensive organizational restructurings. The discourse of stability exists alongside other discourses, some which contradict each other. Together they direct product development and generate meanings. The product developers consequently take an active role in the construction of their work during organizational restructurings. When doing this they also negotiate credible positions for themselves

'... the walls fell down but the blokes just coded ...' - Varieties of stability in software product development during organizational restructurings

Many Finnish IT companies have gone through numerous organizational changes over the past decades. This book draws attention to how stability may be central to software product development experts and IT workers more generally, who continuously have to cope with such change in their workplaces. It does so by analyzing and theorizing change and stability as intertwined and co-existent, thus throwing light on how it is possible that, for example, even if ‘the walls fall down the blokes just code’ and maintain a sense of stability in their daily work. Rather than reproducing the picture of software product development as exciting cutting edge activities and organizational change as dramatic episodes, the study takes the reader beyond the myths surrounding these phenomena to the mundane practices, routines and organizings in product development during organizational change. An analysis of these ordinary practices offers insights into how software product development experts actively engage in constructing stability during organizational change through a variety of practices, including solidarity, homosociality, close relations to products, instrumental or functional views on products, preoccupations with certain tasks and humble obedience. Consequently, the study shows that it may be more appropriate to talk about varieties of stability, characterized by a multitude of practices of stabilizing rather than states of stagnation. Looking at different practices of stability in depth shows the creation of software as an arena for micro-politics, power relations and increasing pressures for order and formalization. The thesis gives particular attention to power relations and processes of positioning following organizational change: how social actors come to understand themselves in the context of ongoing organizational change, how they comply with and/or contest dominant meanings, how they identify and dis-identify with formalization, and how power relations often are reproduced despite dis-identification. Related to processes of positioning, the reader is also given a glimpse into what being at work in a male-dominated and relatively homogeneous work environment looks like. It shows how the strong presence of men or “blokes” of a particular age and education seems to become invisible in workplace talk that appears ‘non-conscious’ of gender.