Analyses of the usefulness of Software Defined Storage Solutions for Web-based Digital Preservation Applications

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

Light and storage on the germination of spores of Dicksonia sellowiana (Presl.) Hook., Dicksoniaceae

Spores of Dicksonia sellowiana are positively photoblastic and reach the maximum percentage of germination at 23 ± 2°C in white light after seven days of imbibition. The pre-induction phase for spores induced by white or red light for 24 hours was 72 hours. Gametophytes grown in white light were plane and bidimensional, while those grown under red light were filamentous. The higher the number of hours of light applied per day during 10 days, the higher the percentage of germination. Germination was higher for long white light treatments applied on a daily basis. The effect of different light intensities on germination was also investigated here. The lower percentages of germination were observed for spores kept under 43% and 2% of full sunlight, while those kept under 26, 19 and 4% presented higher percentages. Spores presented circa 82% of germination after 731 days of storage under refrigeration at aproximately 10°C.

Effect of storage of achenes of Bidens gardneri Baker on light sensitivity during germination

Bidens gardneri is a very common herbaceous species in the cerrados of the state of São Paulo, whose seeds become light sensitive at 25°C only. Achenes of this species were stored in refrigerator at 4°C and in cerrado soil and in forest soil. The field experiments were carried out in the cerrado at the Reserva Biológica e Estação Experimental de Moji Guaçu, in Moji Guaçu and in the forest of the Instituto de Botânica, in São Paulo, Brazil. Achenes of B. gardneri vary in size and achenes from 7 to 12 mm long were used. Achenes stored for up to 6 months at 4°C showed light sensitivity; after 9 months storage, the difference in germination between light and darkness had disappeared for the smallest and the largest achenes used. Seeds of B. gardneri germinated during the period of storage in soil; the number of germinated seeds increased over the storage time, while the number of intact achenes decreased for the same period, no matter if the experiment was being carried out in the cerrado or in the forest. Therefore, the achenes germinated in soil in darkness. Light sensitivity was lost in intact achenes that had been stored in soil for three months.

Storage substances in the androgametogenesis and mature pollen grain of Ilex paraguariensis St. Hil. (Aquifoliaceae)

Storage substances such as starch grains, proteins and lipids were studied during the male gametogenesis and in the mature pollen grain of Ilex paraguariensis St. Hil. (Aquifoliaceae). There are two cycles of amylogenesis and amylolyse. The first cycle lasts until the vacuolated stage when the starch is hydrolyzed and amorphous proteins are stored inside the single vacuole. The next cycle begins after mitosis with the formation of the vegetative and generative cells. At this point, the young vegetative cell stores many starch grains that are bigger than in the first cycle. During the maturation of the male gametophyte, the starch is hydrolyzed and it is absent in the mature pollen grain. Small lipid droplets surround the young generative cell after the mitosis of the androspore and are dispersed in the vegetative cytoplasm during its maturity. The relationship between the pollen storage substances and the ontogeny of the layers in the sporoderm, formation of the generative cell, and the male germ unit were discussed.

Occurrence of xyloglucan containing protuberances in the storage cell walls of cotyledons of Hymenaea courbaril L.

Despite the suggestions of its pectic composition, no clear evidence for this has been presented. Here we show the occurrence of such a structure in walls of cells from cotyledons of Hymenaea courbariI L. These cells are known to accumulate large amounts of storage xyloglucan in the wall and, in this case, the protuberances seem to contain this storage polysaccharide rather than pectin. A hypothetical sequence of events leading from wall strands to protuberances was assembled based on scanning electron microscopy observations. On this basis, a tentative model for how polysaccharides are distributed into the wall, near the regions where protuberances are found, is proposed to explain the presence of storage xyloglucan in their composition.

Effects of moisture content and temperature during storage on germination of the achenes of Bidens gardneri Baker

Bidens gardneri is a herbaceous species of the cerrados, whose seeds are light sensitive at 25 °C, but they become indifferent to light when stored in soil. In this work the effects of moisture content, temperature and light (during storage) upon light sensitivity during germination were studied. Ripe achenes were collected in the cerrados of Itirapina and Moji Guaçu, State of São Paulo, Brazil. The storage conditions of the achenes varied in each experiment. Achenes were stored in darkness or light, in closed bottles, at 4 °C, 20/30 °C or 25 °C. Achenes were imbibed for 24 h at 4 °C, 25 °C or 20/30 °C (in darkness) and then stored for 1, 10, 20, 30 and 40 days (40 days only for 4 °C and 25 °C). Germination tests were conducted at 25 °C and 20/30 °C. The achenes not previously imbibed showed sensitivity to light during germination. High moisture content did not affect light sensitivity of the achenes during germination but high moisture content together with storage temperatures of 25 °C and 20/30 °C had a deleterious effect upon the longevity of the achenes. Alternate temperatures during germination did not change the light sensitivity of newly collected achenes from Itirapina but changed the light sensitivity of the achenes stored imbibed at 4 °C in darkness. Alternate temperatures during storage of achenes with low moisture content did not change their photoblastism when germination was carried out at 25 °C. Alternate temperatures during storage of achenes with high moisture content followed by alternate temperatures during germination changed the light sensitivity of the achenes.

Choosing the target loci : heat shock factors HSF1 and HSF2 as regulators of cell stress and development

Heat shock factors (HSFs) are an evolutionarily well conserved family of transcription factors that coordinate stress-induced gene expression and direct versatile physiological processes in eukaryote organisms. The essentiality of HSFs for cellular homeostasis has been well demonstrated, mainly through HSF1-induced transcription of heat shock protein (HSP) genes. HSFs are important regulators of many fundamental processes such as gametogenesis, metabolic control and aging, and are involved in pathological conditions including cancer progression and neurodegenerative diseases. In each of the HSF-mediated processes, however, the detailed mechanisms of HSF family members and their complete set of target genes have remained unknown. Recently, rapid advances in chromatin studies have enabled genome-wide characterization of protein binding sites in a high resolution and in an unbiased manner. In this PhD thesis, these novel methods that base on chromatin immunoprecipitation (ChIP) are utilized and the genome-wide target loci for HSF1 and HSF2 are identified in cellular stress responses and in developmental processes. The thesis and its original publications characterize the individual and shared target genes of HSF1 and HSF2, describe HSF1 as a potent transactivator, and discover HSF2 as an epigenetic regulator that coordinates gene expression throughout the cell cycle progression. In male gametogenesis, novel physiological functions for HSF1 and HSF2 are revealed and HSFs are demonstrated to control the expression of X- and Y-chromosomal multicopy genes in a silenced chromatin environment. In stressed human cells, HSF1 and HSF2 are shown to coordinate the expression of a wide variety of genes including genes for chaperone machinery, ubiquitin, regulators of cell cycle progression and signaling. These results highlight the importance of cell type and cell cycle phase in transcriptional responses, reveal the myriad of processes that are adjusted in a stressed cell and describe novel mechanisms that maintain transcriptional memory in mitotic cell division.

Germination of spores and growth of gametophytes and sporophytes of Rumohra adiantiformis (Forst.) Ching (Dryopteridaceae) after spore cryogenic storage

Rumohra adiantiformis (Forst.) Ching is a fern (Dryopteridaceae) used in floral arrangements. Spores sterilized in 15% (v/v) solution of commercial sodium hypochlorite for 10 minutes and unsterilized spores were plunged in liquid nitrogen and held for 15 minutes and for 90 days. After the cryogenic treatments, spores were taken out of liquid nitrogen and rapidly thawed out in a water bath or slowly at room temperature and were cultured in Mohr's mineral solution as modified by Dyer, kept at 25 ± 2 ºC and a 16-hours photoperiod. Statistical differences were not observed in the germination of unsterilized spores immersed or not immersed in liquid nitrogen, but when the spores were previously sterilized, a severe inhibition of germination was observed in cryopreserved spores. Faster mean germination time was observed for unsterilized spores cryopreserved in liquid nitrogen for 15 minutes. The germination of spores stored in liquid nitrogen for 90 days reached the maximum percentage after 12 days, while control spores reached their maximum percentage after 16 days. Levels of soluble sugars did not vary among treatments in gametophytes cultivated for 10 weeks after spore inoculation. The number of fronds and the length of the longest frond on sporophytes did not differ statistically among treatments. The relative growth rate of sporophytes grown from cryopreserved and control spores were not statistically different among treatments. Spores of R. adiantiformis immersed in liquid nitrogen for 15 minutes apparently produced phenotypically normal plants.

Diurnal changes in storage carbohydrate metabolism in cotyledons of the tropical tree Hymenaea courbaril L. (Leguminosae)

The cotyledons of Hymenaea courbaril store large amounts of xyloglucan, a cell wall polysaccharide that is believed to serve as storage for the period of seedling establishment. During storage mobilisation, xyloglucan seems to be degraded by a continuous process that starts right after radicle protrusion and follows up to the establishment of photosynthesis. Here we show evidence that events related to the hydrolases activities and production (α-xylosidase, β-galactosidase, β-glucosidase and xyloglucan endo-β-transglucosilase) as well as auxin, showed changes that follow the diurnal cycle. The period of higher hydrolases activities was between 6pm and 6am, which is out of phase with photosynthesis. Among the enzymes, α-xilosidase seems to be more important than β-glucosidase and β-galactosidase in the xyloglucan disassembling mechanism. Likewise, the sugars related with sucrose metabolism followed the rhythm of the hydrolases, but starch levels were shown to be practically constant. A high level of auxin was observed during the night, what is compatible with the hypothesis that this hormone would be one of the regulators of the whole process. The probable biological meaning of the existence of such a complex control mechanism during storage mobilisation is likely to be related to a remarkably high level of efficiency of carbon usage by the growing seedling of Hymenaea courbaril, allowing the establishment of very vigorous seedlings in the tropical forest.

Characteristics of urban heat island (UHI) in a high latitude coastal city - a case study of Turku, SW Finland

The term urban heat island (UHI) refers to the common situation in which the city is warmer than its rural surroundings. In this dissertation, the local climate, and especially the UHI, of the coastal city of Turku (182,000 inh.), SW Finland, was studied in different spatial and temporal scales. The crucial aim was to sort out the urban, topographical and water body impact on temperatures at different seasons and times of the day. In addition, the impact of weather on spatiotemporal temperature differences was studied. The relative importance of environmental factors was estimated with different modelling approaches and a large number of explanatory variables with various spatial scales. The city centre is the warmest place in the Turku area. Temperature excess relative to the coldest sites, i.e. rural areas about 10 kilometers to the NE from the centre, is on average 2 °C. Occasionally, the UHI intensity can be even 10 °C. The UHI does not prevail continuously in the Turku area, but occasionally the city centre can be colder than its surroundings. Then the term urban cool island or urban cold island (UCI) is used. The UCI is most common in daytime in spring and in summer, whereas during winter the UHI prevails throughout the day. On average, the spatial temperature differences are largest in summer, whereas the single extreme values are often observed in winter. The seasonally varying sea temperature causes the shift of relatively warm areas towards the coast in autumn and inland in spring. In the long term, urban land use was concluded to be the most important factor causing spatial temperature differences in the Turku area. The impact was mainly a warming one. The impact of water bodies was emphasised in spring and autumn, when the water temperature was relatively cold and warm, respectively. The impact of topography was on average the weakest, and was seen mainly in proneness of relatively low-lying places for cold air drainage during night-time. During inversions, however, the impact of topography was emphasised, occasionally outperforming those of urban land use and water bodies.

Effect of collection, transport, processing and storage of blood specimens on the activity of lysosomal enzymes in plasma and leukocytes

This study was designed to evaluate the effect of different conditions of collection, transport and storage on the quality of blood samples from normal individuals in terms of the activity of the enzymes ß-glucuronidase, total hexosaminidase, hexosaminidase A, arylsulfatase A and ß-galactosidase. The enzyme activities were not affected by the different materials used for collection (plastic syringes or vacuum glass tubes). In the evaluation of different heparin concentrations (10% heparin, 5% heparin, and heparinized syringe) in the syringes, it was observed that higher doses resulted in an increase of at least 1-fold in the activities of ß-galactosidase, total hexosaminidase and hexosaminidase A in leukocytes, and ß-glucuronidase in plasma. When the effects of time and means of transportation were studied, samples that had been kept at room temperature showed higher deterioration with time (72 and 96 h) before processing, and in this case it was impossible to isolate leukocytes from most samples. Comparison of heparin and acid citrate-dextrose (ACD) as anticoagulants revealed that ß-glucuronidase and hexosaminidase activities in plasma reached levels near the lower normal limits when ACD was used. In conclusion, we observed that heparin should be used as the preferable anticoagulant when measuring these lysosomal enzyme activities, and we recommend that, when transport time is more than 24 h, samples should be shipped by air in a styrofoam box containing wet ice.

Working fluid selection and design of small-scale waste heat recovery systems based on organic Rankine cycles

Demand for the use of energy systems, entailing high efficiency as well as availability to harness renewable energy sources, is a key issue in order to tackling the threat of global warming and saving natural resources. Organic Rankine cycle (ORC) technology has been identified as one of the most promising technologies in recovering low-grade heat sources and in harnessing renewable energy sources that cannot be efficiently utilized by means of more conventional power systems. The ORC is based on the working principle of Rankine process, but an organic working fluid is adopted in the cycle instead of steam. This thesis presents numerical and experimental results of the study on the design of small-scale ORCs. Two main applications were selected for the thesis: waste heat re- covery from small-scale diesel engines concentrating on the utilization of the exhaust gas heat and waste heat recovery in large industrial-scale engine power plants considering the utilization of both the high and low temperature heat sources. The main objective of this work was to identify suitable working fluid candidates and to study the process and turbine design methods that can be applied when power plants based on the use of non-conventional working fluids are considered. The computational work included the use of thermodynamic analysis methods and turbine design methods that were based on the use of highly accurate fluid properties. In addition, the design and loss mechanisms in supersonic ORC turbines were studied by means of computational fluid dynamics. The results indicated that the design of ORC is highly influenced by the selection of the working fluid and cycle operational conditions. The results for the turbine designs in- dicated that the working fluid selection should not be based only on the thermodynamic analysis, but requires also considerations on the turbine design. The turbines tend to be fast rotating, entailing small blade heights at the turbine rotor inlet and highly supersonic flow in the turbine flow passages, especially when power systems with low power outputs are designed. The results indicated that the ORC is a potential solution in utilizing waste heat streams both at high and low temperatures and both in micro and larger scale appli- cations.

Vicilins (7S storage globulins) of cowpea (Vigna unguiculata) seeds bind to chitinous structures of the midgut of Callosobruchus maculatus (Coleoptera: Bruchidae) larvae

The presence of chitin in midgut structures of Callosobruchus maculatus larvae was shown by chemical and immunocytochemical methods. Detection by Western blotting of cowpea (Vigna unguiculata) seed vicilins (7S storage proteins) bound to these structures suggested that C. maculatus-susceptible vicilins presented less staining when compared to C. maculatus-resistant vicilins. Storage proteins present in the microvilli in the larval midgut of the bruchid were recognized by immunolabeling of vicilins in the appropriate sections with immunogold conjugates. These labeling sites coincided with the sites labeled by an anti-chitin antibody. These results, taken together with those previously published showing that the lower rates of hydrolysis of variant vicilins from C. maculatus-resistant seeds by the insect's midgut proteinases and those showing that vicilins bind to chitin matrices, may explain the detrimental effects of variant vicilins on the development of C. maculatus larvae.

Analysis and modelling of chemical looping combustion process with and without oxygen uncoupling

Effective control and limiting of carbon dioxide (CO₂) emissions in energy production are major challenges of science today. Current research activities include the development of new low-cost carbon capture technologies, and among the proposed concepts, chemical combustion (CLC) and chemical looping with oxygen uncoupling (CLOU) have attracted significant attention allowing intrinsic separation of pure CO₂ from a hydrocarbon fuel combustion process with a comparatively small energy penalty. Both CLC and CLOU utilize the well-established fluidized bed technology, but several technical challenges need to be overcome in order to commercialize the processes. Therefore, development of proper modelling and simulation tools is essential for the design, optimization, and scale-up of chemical looping-based combustion systems. The main objective of this work was to analyze the technological feasibility of CLC and CLOU processes at different scales using a computational modelling approach. A onedimensional fluidized bed model frame was constructed and applied for simulations of CLC and CLOU systems consisting of interconnected fluidized bed reactors. The model is based on the conservation of mass and energy, and semi-empirical correlations are used to describe the hydrodynamics, chemical reactions, and transfer of heat in the reactors. Another objective was to evaluate the viability of chemical looping-based energy production, and a flow sheet model representing a CLC-integrated steam power plant was developed. The 1D model frame was succesfully validated based on the operation of a 150 kWth laboratory-sized CLC unit fed by methane. By following certain scale-up criteria, a conceptual design for a CLC reactor system at a pre-commercial scale of 100 MWth was created, after which the validated model was used to predict the performance of the system. As a result, further understanding of the parameters affecting the operation of a large-scale CLC process was acquired, which will be useful for the practical design work in the future. The integration of the reactor system and steam turbine cycle for power production was studied resulting in a suggested plant layout including a CLC boiler system, a simple heat recovery setup, and an integrated steam cycle with a three pressure level steam turbine. Possible operational regions of a CLOU reactor system fed by bituminous coal were determined via mass, energy, and exergy balance analysis. Finally, the 1D fluidized bed model was modified suitable for CLOU, and the performance of a hypothetical 500 MWth CLOU fuel reactor was evaluated by extensive case simulations.

Excitotoxic median raphe lesions aggravate working memory storage performance deficits caused by scopolamine infusion into the dentate gyrus of the hippocampus in the inhibitory avoidance task in rats

The interactions between the median raphe nucleus (MRN) serotonergic system and the septohippocampal muscarinic cholinergic system in the modulation of immediate working memory storage performance were investigated. Rats with sham or ibotenic acid lesions of the MRN were bilaterally implanted with cannulae in the dentate gyrus of the hippocampus and tested in a light/dark step-through inhibitory avoidance task in which response latency to enter the dark compartment immediately after the shock served as a measure of immediate working memory storage. MRN lesion per se did not alter response latency. Post-training intrahippocampal scopolamine infusion (2 and 4 µg/side) produced a more marked reduction in response latencies in the lesioned animals compared to the sham-lesioned rats. Results suggest that the immediate working memory storage performance is modulated by synergistic interactions between serotonergic projections of the MRN and the muscarinic cholinergic system of the hippocampus.