DNA Packaging and Host Cell Lysis: Late Events in Bacteriophage PRD1 Infection

The object of this study is a tailless internal membrane-containing bacteriophage PRD1. It has a dsDNA genome with covalently bound terminal proteins required for replication. The uniqueness of the structure makes this phage a desirable object of research. PRD1 has been studied for some 30 years during which time a lot of information has accumulated on its structure and life-cycle. The two least characterised steps of the PRD1 life-cycle, the genome packaging and virus release are investigated here. PRD1 shares the main principles of virion assembly (DNA packaging in particular) and host cell lysis with other dsDNA bacteriophages. However, this phage has some fascinating individual peculiarities, such as DNA packaging into a membrane vesicle inside the capsid, absence of apparent portal protein, holin inhibitor and procapsid expansion. In the course of this study we have identified the components of the DNA packaging vertex of the capsid, and determined the function of protein P6 in packaging. We managed to purify the procapsids for an in vitro packaging system, optimise the reaction and significantly increase its efficiency. We developed a new method to determine DNA translocation and were able to quantify the efficiency and the rate of packaging. A model for PRD1 DNA packaging was also proposed. Another part of this study covers the lysis of the host cell. As other dsDNA bacteriophages PRD1 has been proposed to utilise a two-component lysis system. The existence of this lysis system in PRD1 has been proven by experiments using recombinant proteins and the multi-step nature of the lysis process has been established.

Late Quaternary vegetational and climatic changes from tropical peats in southern India - An extended record up to 40,000 years BP

Stable carbon isotope ratios of peats dated (by C-14) back to 40 kyr BP from the montane region (> 1800 m asl) of the Nilgiris, southern India, reflect changes in the relative proportions of C3 and C4 plant types, which are influenced by soil moisture (and hence monsoonal precipitation), From prior to 40 kyr BP until 28 kyr BP, a general decline in delta(13)C values from about - 14 per mil to - 19 per mil suggests increased dominance of C3 plants concurrent with increasingly moist conditions, During 28-18 kyr BP there seems relatively little change with delta(13) C of - 19 to - 18 per mil, At about 16 kyr BP a sharp reversal in delta(13)C to a peak of - 14.7 per mil indicates a clear predominance of C4 vegetation associated with arid conditions, possibly during or just after the Last Glacial Maximum, A moist phase at about 9 kyr BP (the Holocene Optimum) with dominance of C3 vegetation type is observed, while arid conditions are re-established during 5-2 kyr BP with an overall dominance of C4 vegetation, New data do not support the occurrence of a moist phase coinciding with the Mediaeval Warm Period (at 0.6 kyr BP) as suggested earlier, Overall, the climate and vegetation in the high altitude regions of the southern Indian tropics seem to have responded to past global climatic changes, and this is consistent with other evidences from India and other tropical regions.

Early and late electrophysiological effects of distractor frequency in picture naming: Reconciling input and output accounts

The “distractor-frequency effect” refers to the finding that high-frequency (HF) distractor words slow picture naming less than low-frequency distractors in the picture–word interference paradigm. Rival input and output accounts of this effect have been proposed. The former attributes the effect to attentional selection mechanisms operating during distractor recognition, whereas the latter attributes it to monitoring/decision mechanisms operating on distractor and target responses in an articulatory buffer. Using high-density (128-channel) EEG, we tested hypotheses from these rival accounts. In addition to conducting stimulus- and response-locked whole-brain corrected analyses, we investigated the correct-related negativity, an ERP observed on correct trials at fronto-central electrodes proposed to reflect the involvement of domain general monitoring. The wholebrain ERP analysis revealed a significant effect of distractor frequency at inferior right frontal and temporal sites between 100 and 300-msec post-stimulus onset, during which lexical access is thought to occur. Response-locked, region of interest (ROI) analyses of fronto-central electrodes revealed a correct-related negativity starting 121 msec before and peaking 125 msec after vocal onset on the grand averages. Slope analysis of this component revealed a significant difference between HF and lowfrequency distractor words, with the former associated with a steeper slope on the time windowspanning from100 msec before to 100 msec after vocal onset. The finding of ERP effects in time windows and components corresponding to both lexical processing and monitoring suggests the distractor frequency effect is most likely associated with more than one physiological mechanism.

Mitochondrial helicase Twinkle in mtDNA copy number regulation and a late-onset disease model

Mitochondrial diseases are caused by disturbances of the energy metabolism. The disorders range from severe childhood neurological diseases to muscle diseases of adults. Recently, mitochondrial dysfunction has also been found in Parkinson s disease, diabetes, certain types of cancer and premature aging. Mitochondria are the power plants of the cell but they also participate in the regulation of cell growth, signaling and cell death. Mitochondria have their own genetic material, mtDNA, which contains the genetic instructions for cellular respiration. Single cell may host thousands of mitochondria and several mtDNA molecules may reside inside single mitochondrion. All proteins needed for mtDNA maintenance are, however, encoded by the nuclear genome, and therefore, mutations of the corresponding genes can also cause mitochondrial disease. We have here studied the function of mitochondrial helicase Twinkle. Our research group has previously identified nuclear Twinkle gene mutations underlying an inherited adult-onset disorder, progressive external ophthalmoplegia (PEO). Characteristic for the PEO disease is the accumulation of multiple mtDNA deletions in tissues such as the muscle and brain. In this study, we have shown that Twinkle helicase is essential for mtDNA maintenance and that it is capable of regulating mtDNA copy number. Our results support the role of Twinkle as the mtDNA replication helicase. No cure is available for mitochondrial disease. Good disease models are needed for studies of the cause of disease and its progression and for treatment trials. Such disease model, which replicates the key features of the PEO disease, has been generated in this study. The model allows for careful inspection of how Twinkle mutations lead to mtDNA deletions and further causes the PEO disease. This model will be utilized in a range of studies addressing the delay of the disease onset and progression and in subsequent treatment trials. In conclusion, in this thesis fundamental knowledge of the function of the mitochondrial helicase Twinkle was gained. In addition, the first model for adult-onset mitochondrial disease was generated.

Late results after paediatric cardiac surgery

Background: Congenital heart defects include a wide range of inborn malformations. Depending on the defect, the life expectancy of a newborn with cardiac anomaly varies from a few days to a normal life span. In most instances surgery, is the only treatment available. The late results of surgery have not been comprehensively investigated. Aims: Mortality, morbidity and the life situation of all Finnish patients who had been operated on for congenital heart defect during childhood were investigated. Methods: Patient and surgical data were gathered from all hospitals that had performed heart surgeries on children. Late mortality and survival data were obtained from the population registry, and the causes of deaths from Statistics Finland. Morbidity of patients operated on during 1953-1989 was assessed by the usage of medicines. The pharmacotherapy data of patients and controls were obtained from the Social Insurance Institute. The life situation of patients was surveyed by mailed questionnaire. Survival, causes of deaths and life situation of patients were compared with those of the general population. Results: A total of 7240 cardiac operations were performed on 6461 children during the first 37 years of cardiac surgery (1953-1989). The number of procedures constantly rose during this period, and the increase continued in later years. The patient material varied over time, as more defects became surgically treatable. During 1953-1989 the operative mortality (death within 30 days of surgery) was 6.9%. In the 1990s a slight rise occurred in early mortality, as increasingly complicated patients were surgically treated. During 2000-2003 practically no defects were beyond the operative range. Thus, the operative mortality of 4.4% was excellent, decreasing even further to 2.0% in 2004-2007. The overall 45-year survival of patients operated on in 1953-1989 was 78%, and the corresponding figure for the general population was 93%. Survival depended on the defect, being worst among patients with univentricular heart. Late survival was also better during the 1990s and at the beginning of the 21st century. Of the 6028 early survivors, 592 died late (>30 days) after surgery. A total of 397 deaths (67%) were related and 185 (31%) unrelated to congenital heart defect. The cause of death was unknown in 10 cases. Of those 5774 patients who survived their first operation and had complete follow-up, 16% were operated on several times. Seventeen percent of patients used medicines for cardiac symptoms (heart failure, arrhythmia, hypertension and coronary disease). Patients risk of using cardiac medicines was 2.16 (Cl 1.97-2.37) times higher than that of controls. Patients also had more genetic syndromes and mental retardation and more often used medicines for asthma and epilepsy. Adult patients who had been operated on as children had coped surprisingly well with their defects. Their level of education was similar and their employment level even higher than expected, and they were living in a steady relationship as often as the general population. Conclusions: Cardiac surgery developed rapidly, and nowadays practically all defects can be treated. The overall survival of all operated patients was 78%, 16% less than that of the general population. However, it was significantly better than the anticipated natural survival. However, many patients had health problems; 16% needed reoperations and 17% cardiac medicines to maintain their condition. Most of the patients assessed their general health as good and lived a normal life.

Evolution of isolated streamwise vortices in the late stages of boundary layer transition

Experiments were conducted with two, smooth hills, lying well within the boundary layer over a flat plate mounted in a wind tunnel. One hill was shallow, with peak height 1.5 mm and width 50 mm; the other, steep, 3 mm high and 30 mm wide. Since the hills occupied one-half of the tunnel span, streamwise vorticity formed near the hills' edge. At a freestream speed of 3.5 m/s, streaks formed with inflectional wall-normal and spanwise velocity profiles but without effecting transition. Transition, observed at 7.5 m/s, took different routes with the two hills. With the steep hill, streamwise velocity signals exhibited the passage of a wave packet which intensified before breakdown to turbulence. With the shallow hill there was a broad range of frequencies present immediately downstream of the hill. These fluctuations grew continuously and transition occurred within a shorter distance. Since the size of the streamwise vorticity generated at the hill edge is of the order of the hill height, the shallow hill generates vorticity closer to the wall and supports an earlier transition, whereas the steep hill creates a thicker vortex and associated streaks which exhibit oscillations due to their own instability as an additional precursor stage before transition.

Sterol-binding proteins in late endosomes : Regulation of endosome motility and lipid metabolism

Despite its bad reputation in the mass media, cholesterol is an indispensable constituent of cellular membranes and vertebrate life. It is, however, also potentially lethal as it may accumulate in the arterial intima causing atherosclerosis or elsewhere in the body due to inherited conditions. Studying cholesterol in cells, and research on how the cell biology of cholesterol affects on system level is essential for a better understanding of the disease states associated with cholesterol and for the development of new therapies for these conditions. On its way to the cell, exogenous cholesterol traverses through endosomes, transport vesicles involved in internalizing material to cells, and needs to be transported out of this compartment. This endosomal pool of cholesterol is important for understanding both the common disorders of metabolism and the more rare hereditary disorders of cholesterol metabolism. The study of cholesterol in cells has been hampered by the lack of bright fluorescent sterol analogs that would resemble cholesterol enough to be used in cellular studies. In the first study of my thesis, we present a new sterol analog, Boron-Dipyrromethene (BODIPY)-cholesterol for visualizing sterols in living cells and organism. This fluorescent cholesterol derivative is shown to behave similarly to cholesterol both by atomic scale computer simulations and biochemical experiments. We characterize its localization inside different types of living cells and show that it can be used to study sterol trafficking in living organisms. Two sterol binding proteins associated with the endosomal membrane; the Niemann-Pick type C disease protein 1 (NPC1) and the Oxysterol Binding Protein Related Protein 1 (ORP1) are the subjects of the rest of this study. Sensing cholesterol on endosomes, transporting lipids away from this compartment and the effects these lipids play on cellular metabolism are considered. In the second study we characterize how the NPC1 protein affects lipid metabolism. We show that this cholesterol binding protein affects synthesis of triglycerides and that genetic polymorphisms or a genetic defect in the NPC1 gene affect triglyceride on the whole body level. These effects take place via regulation of carbon fluxes to different lipid classes in cells. In the third part we characterize the effects of another endosomal sterol binding protein, ORP1L on the function and motility of endosomes. Specifically we elucidate how a mutation in the ability of ORP1L to bind sterols affects its behavior in cells, and how a change in ORP1L levels in cells affects the localization, degradative capacity and motility of endosomes. In addition we show that ORP1L manipulations affect cholesterol balance also in macrophages, a cell type important for the development of atherosclerosis.

Global capitalism meets national spirit: Discourses in media texts on a cross-border acquisition

In this article, the authors explore media coverage of a recent acquisition across national borders. Their starting point is that the media represent a key arena of “discursive strategizing” for actors such as corporate managers. They illustrate and specify how global capitalism, as discourse relying on economic and financial rationale and exemplified here by the acquiring firm’s attempts to expand, meets national spirit, exemplified here by the complexity in selling the acquisition target to foreigners. The main contribution of this study lies in identifying how key actors draw on and mobilize rationalistic and nationalistic discourses in public discussion. The analysis illustrates that the same actors can draw on different—even contradictory—discourses at different points in time. Furthermore, different actors—even with opposing objectives—may draw on the same discourse in legitimizing their positions and pursuing specific ends.

Late Svecofennian leucogranites of southern Finland : Chronicles of an orogenic collapse

Leucogranite magmatism occurred in southern Finland during the later stages of the Paleoproterozoic Svecofennian orogeny. The leucogranites are considered to have formed from pre-existing crustal rocks that have undergone anatexis in the extensional stage of the orogeny, following continental collision and resultant crustal thickening. The leucogranites have been studied in the field using petrographic and mineralogical methods, elemental and isotope geochemistry on whole rocks and minerals, and U-Pb geochronology. On outcrop scale, these granites typically form heterogeneous, layered, sheet-like bodies that migmatize their country rocks. All of the leucogranites are peraluminous and rich in SiO2, but otherwise display significant geochemical variation. Their Nd isotope composition ranges from fairly juvenile to very unradiogenic, and the Hf isotope composition of their zircon shows a varying degree of mixing in the source, the zircon populations becoming more heterogeneous and generally less radiogenic towards the east. The leucogranites have been dated using U-Pb isotopic analyses, utilizing thermal ionization mass spectrometry, secondary ion mass spectrometry, and laser ablation multicollector ICP mass spectrometry on zircon and monazite. The results show that the granites were emplaced between 1.85 Ga and 1.79 Ga, which is a considerably longer period than has traditionally been perceived for these rocks. The rocks tend to become younger towards the east. Single crystal data also display a wide array of inherited zircons, especially in the eastern part of the leucogranite belt. The most common inherited age groups are ~2.8 2.5 Ga, ~2.1 2.1 Ga, and ~1.9 Ga. Magmatic zircon and monazite usually record similar ages for any one sample.Thermobarometric calculations indicate that the leucogranites in the Veikkola area of southcentral Finland were formed from relatively low-temperature melts, and emplaced at 17-25 km depth, i.e. at mid-crustal level. It is likely that these conditions apply to the Svecofennian leucogranites in general. Large differences in the Hf and Nd isotope compositions, emplacement ages, and distributions of inherited zircon ages show that these granites were formed from different types of source rocks, which probably included both sedimentary and igneous rocks.

Evil Gods and Reckless Saviours : Adaptation and Appropriation in Late Twentieth Century Jesus-Novels

Late twentieth century Jesus-novels search after a completely new picture of Jesus. Novels written for instance by Norman Mailer, José Saramago, Michèle Roberts, Marianne Fredriksson, and Ki Longfellow provide an inversive revision of the canonic Gospels. They read the New Testament in terms of the present age. In their adaptation the story turns often into a critique of the whole Christian history. The investigated contrast-novels end up with an appropriation that is based on prototypical rewriting. They aim at the rehabilitation of Judas, and some of them make Mary Magdalane the key figure of Christianity. Saramago describes God as a blood thirsty tyrant, and Mailer makes God combat with the Devil in a manichean sense as with an equal. Such ideas are familiar both from poststructuralist philosophy and post-metaphysical death-of-God theology. The main result of the intertextual analysis is that these scholars have adopted Nietzschean ideas in their writing. Quite unlike earlier Jesus-novels, these more recent novels present a revision that produces discontinuity with the original source text, the New Testament. The intertextual strategy is based on contradiction. The reader wittnesses contesting and challenging, the authors attack Biblical beliefs and attempt to dissolve Christian doctrines. An attack on Biblical slave morality and violent concept of God deprives Jesus of his Jewish Messianic identity, makes Old Testament law a contradiction of life, calls sacrificial soteriology a violent pattern supporting oppression, and presents God as a cruel monster who enslaves people under his commandments and wishes their death. The new Jesus-figure contests Mosaic Law, despises orthodox Judaism, abandons Jewish customs and even questions Old Testament monotheism. In result, the novels intentionally transfer Jesus out of Judaism. Furthermore, Jewish faith appears in a negative light. Such an intertextual move is not open anti-Semitism but it cannot avoid attacking Jewish worship. Why? One reason that explains these attitudes is that Western culture still carries anti-Judaic attitudes beneath the surface covered with sentiments of equality and tolerance. Despite the evident post-holocaust consciousness present in the novels, they actually adopt an arrogant and ironical refutation of Jewish beliefs and Old Testament faith. In these novels, Jesus is made a complete opposite and antithesis to Judaism. Key words: Jesus-novel, intertextuality, adaptation, slave morality, Nietzsche, theodicy, patriarchy.

Magnetic fabrics indicating Late Quaternary seismicity in the Himalayan foothills

The anisotropy of magnetic susceptibility (AMS) study was performed on soft sediment samples from a trenched fault zone across the Himalayan frontal thrust (HFT), western Himalaya. AMS orientation of K-min axes in the trench sediments is consistent with lateral shortening revealed by geometry of deformed regional structures and recent earthquakes. Well-defined vertical magnetic foliation parallel to the flexure cleavage in which a vertical magnetic lineation is developed, high anisotropy, and triaxial ellipsoids suggest large overprinting of earth-quake- related fabrics. The AMS data suggest a gradual variation from layer parallel shortening (LPS) at a distance from the fault trace to a simple shear fabric close to the fault trace. An abrupt change in the shortening direction (K-min) from NE-SW to E-W suggests a juxtaposition of pre-existing layer parallel shortening fabric, and bending-related flexure associated with an earthquake. Hence the orientation pattern of magnetic susceptibility axes helps in identifying co-seismic structures in Late Holocene surface sediments.