What was behind the bark? : An assessment of decay among urban Tilia, Betula and Acer trees felled as hazardous in the Helsinki City area

Old trees growing in urban environments are often felled due to symptoms of mechanical defects that could be hazardous to people and property. The decisions concerning these removals are justified by risk assessments carried out by tree care professionals. The major motivation for this study was to determine the most common profiles of potential hazard characteristics for the three most common urban tree genera in Helsinki City: Tilia, Betula and Acer, and in this way improve management practices and protection of old amenity trees. For this research, material from approximately 250 urban trees was collected in cooperation with the City of Helsinki Public Works Department during 2001 - 2004. From the total number of trees sampled, approximately 70% were defined as hazardous. The tree species had characteristic features as potential hazard profiles. For Tilia trees, hollowed heartwood with low fungal activity and advanced decay caused by Ganoderma lipsiense were the two most common profiles. In Betula spp., the primary reason for tree removal was usually lowered amenity value in terms of decline of the crown. Internal cracks, most often due to weak fork formation, were common causes of potential failure in Acer spp. Decay caused by Rigidoporus populinus often increased the risk of stem breakage in these Acer trees. Of the decay fungi observed, G. lipsiense was most often the reason for the increased risk of stem collapse. Other fungi that also caused extensive decay were R. populinus, Inonotus obliquus, Kretzschmaria deusta and Phellinus igniarius. The most common decay fungi in terms of incidence were Pholiota spp., but decay caused by these species did not have a high potential for causing stem breakage, because it rarely extended to the cambium. The various evaluations used in the study suggested contradictions in felling decisions based on trees displaying different stages of decay. For protection of old urban trees, it is crucial to develop monitoring methods so that tree care professionals could better analyse the rate of decay progression towards the sapwood and separate those trees with decreasing amounts of sound wood from those with decay that is restricted to the heartwood area.

Role of heat treatment in the processing and quality of oat flakes

This thesis reports on investigations into the influence of heat treatment on the manufacturing of oat flakes. Sources of variation in the oat flake quality are reviewed, including the whole chain from the farm to the consumer. The most important quality parameters of oat flakes are the absence of lipid hydrolysing enzymes, specific weight, thickness, breakage (fines), water absorption. Flavour, colour and pasting properties are also important, but were not included in the experimental part of this study. Of particular interest was the role of heat processing. The first possible heat treatment may occur already during grain drying, which in Finland generally happens at the farm. At the mill, oats are often kilned to stabilise the product by inactivating lipid hydrolysing enzymes. Almost invariably steaming is used during flaking, to soften the groats and reduce flake breakage. This thesis presents the use of a material science approach to investigating a complex system, typical of food processes. A combination of fundamental and empirical rheological measurements was used together with a laboratory scale process to simulate industrial processing. The results were verified by means of industrial trials. Industrially produced flakes at three thickness levels (nominally 0.75, 0.85 and 0.90 mm) were produced from kilned and unkilned oat groats, and the flake strength was measured at different moisture contents. Kilning was not found to significantly affect the force required to puncture a flake with a 2mm cylindrical probe, which was taken as a measure of flake strength. To further investigate how heat processing contributes to flake quality, dynamic mechanical analysis was used to characterise the effect of heat on the mechanical properties of oats. A marked stiffening of the groat, of up to about 50% increase in storage modulus, was observed during first heating at around 36 to 57°C. This was also observed in tablets prepared from ground groats and extracted oat starch. This stiffening was thus attributed to increased adhesion between starch granules. Groats were steamed in a laboratory steamer and were tempered in an oven at 80 110°C for 30 90 min. The maximum force required to compress the steamed groats to 50% strain increased from 50.7 N to 57.5 N as the tempering temperature was increased from 80 to 110°C. Tempering conditions also affected water absorption. A significantly higher moisture content was observed for kilned (18.9%) compared to unkilned (17.1%) groats, but otherwise had no effect on groat height, maximum force or final force after a 5 s relaxation time. Flakes were produced from the tempered groats using a laboratory flaking machine, using a roll gap of 0.4 mm. Apart from specific weight, flake properties were not influenced by kilning. Tempering conditions however had significant effects on the specific weight, thickness and water absorption of the flakes, as well as on the amount of fine material (<2 mm) produced during flaking. Flake strength correlated significantly with groat strength and flake thickness. Trial flaking at a commercial mill confirmed that groat temperature after tempering influenced water absorption. Variation in flake strength was observed , but at the groat temperatures required to inactivate lipase, it was rather small. Cold flaking of groats resulted in soft, floury flakes. The results presented in this thesis suggest that heating increased the adhesion between starch granules. This resulted in an increase in the stiffness and brittleness of the groat. Brittle fracture, rather than plastic flow, during flaking could result in flaws and cracks in the flake. These would be expected to increase water absorption. This was indeed observed as tempering temperature increased. Industrial trials, conducted with different groat temperatures, confirmed the main findings of the laboratory experiments. The approach used in the present study allowed the systematic study of the effect of interacting process parameters on product quality. There have been few scientific studies of oat processing, and these results can be used to understand the complex effects of process variables on flake quality. They also offer an insight into what happens as the oat groat is deformed into a flake.

Characterization of the molecular components and function of BARE-1, Hin-Mu and Mu transposition machineries

Transposable elements, transposons, are discrete DNA segments that are able to move or copy themselves from one locus to another within or between their host genome(s) without a requirement for DNA homology. They are abundant residents in virtually all the genomes studied, for instance, the genomic portion of TEs is approximately 3% in Saccharomyces cerevisiae, 45% in humans, and apparently more than 70% in some plant genomes such as maize and barley. Transposons plays essential role in genome evolution, in lateral transfer of antibiotic resistance genes among bacteria and in life cycle of certain viruses such as HIV-1 and bacteriophage Mu. Despite the diversity of transposable elements they all use a fundamentally similar mechanism called transpositional DNA recombination (transposition) for the movement within and between the genomes of their host organisms. The DNA breakage and joining reactions that underlie their transposition are chemically similar in virtually all known transposition systems. The similarity of the reactions is also reflected in the structure and function of the catalyzing enzymes, transposases and integrases. The transposition reactions take place within the context of a transposition machinery, which can be particularly complex, as in the case of the VLP (virus like particle) machinery of retroelements, which in vivo contains RNA or cDNA and a number of element encoded structural and catalytic proteins. Yet, the minimal core machinery required for transposition comprises a multimer of transposase or integrase proteins and their binding sites at the element DNA ends only. Although the chemistry of DNA transposition is fairly well characterized, the components and function of the transposition machinery have been investigated in detail for only a small group of elements. This work focuses on the identification, characterization, and functional studies of the molecular components of the transposition machineries of BARE-1, Hin-Mu and Mu. For BARE-1 and Hin-Mu transpositional activity has not been shown previously, whereas bacteriophage Mu is a general model of transposition. For BARE-1, which is a retroelement of barley (Hordeum vulgare), the protein and DNA components of the functional VLP machinery were identified from cell extracts. In the case of Hin-Mu, which is a Mu-like prophage in Haemophilus influenzae Rd genome, the components of the core machinery (transposase and its binding sites) were characterized and their functionality was studied by using an in vitro methodology developed for Mu. The function of Mu core machinery was studied for its ability to use various DNA substrates: Hin-Mu end specific DNA substrates and Mu end specific hairpin substrates. The hairpin processing reaction by MuA was characterized in detail. New information was gained of all three machineries. The components or their activity required for functional BARE-1 VLP machinery and retrotransposon life cycle were present in vivo and VLP-like structures could be detected. The Hin-Mu core machinery components were identified and shown to be functional. The components of the Mu and Hin-Mu core machineries were partially interchangeable, reflecting both evolutionary conservation and flexibility within the core machineries. The Mu core machinery displayed surprising flexibility in substrate usage, as it was able to utilize Hin-Mu end specific DNA substrates and to process Mu end DNA hairpin substrates. This flexibility may be evolutionarily and mechanistically important.

Human trypsinogens in the pancreas and in cancer

Human pancreatic juice contains two major trypsinogen isoenzymes called trypsinogen-1 and -2, or cationic and anionic trypsinogen, respectively. Trypsinogen isoenzymes are also expressed in various normal and malignant tissues. We aimed at developing monoclonal antibodies (MAbs) and time-resolved immunofluorometric methods recognizing human trypsinogen-1 and -2, respectively. Using these MAbs and methods we purified, characterized and quantitated trypsinogen isoenzymes in serum samples, ovarian cyst fluids and conditioned cell culture media. In sera from healthy subjects and patients with extrapancreatic disease the concentration of trypsinogen-1 is higher than that of trypsinogen-2. However, in acute pancreatitis we found that the concentration of serum trypsinogen-2 is 50-fold higher than in controls, whereas the difference in trypsinogen-1 concentration is only 15-fold. This suggested that trypsinogen-2 could be used as a diagnostic marker for acute pancreatitis. In human ovarian cyst fluids tumor-associated trypsinogen-2 (TAT-2) is the predominant isoenzyme. Most notably, in mucinous cyst fluids the levels of TAT-2 were higher in borderline and malignant than in benign cases. The increased levels in association with malignancy suggested that TAT could be involved in ovarian tumor dissemination and breakage of tissue barriers. Serum samples from patients who had undergone pancreatoduodenectomy contained trypsinogen-2. Trypsinogen-1 was detected in only one of nine samples. These results suggested that the expression of trypsinogen is not restricted to the pancreas. Determination of the isoenzyme pattern by ion exchange chromatography revealed isoelectric variants of trypsinogen isoenzymes in serum samples. Intact trypsinogen isoenzymes and tryptic and chymotryptic trypsinogen peptides were purified and characterized by mass spectrometry, Western blot analysis and N-terminal sequencing. The results showed that pancreatic trypsinogen-1 and -2 are sulfated at tyrosine 154 (Tyr154), whereas TAT-2 from a colon carcinoma cell line is not. Tyr154 is located within the primary substrate binding pocket of trypsin, thus Tyr154 sulfation is likely to influence substrate binding. The previously known differences in charge, substrate specificity and inhibitor binding between pancreatic and tumor-associated trypsinogens are suggested to be caused by sulfation of Tyr154 in pancreatic trypsinogens.

Towards Understanding Powder Behavior Via Simulation

The aim of this study was to investigate powder and tablet behavior at the level of mechanical interactions between single particles. Various aspects of powder packing, mixing, compression, and bond formation were examined with the aid of computer simulations. The packing and mixing simulations were based on spring forces interacting between particles. Packing and breakage simulations included systems in which permanent bonds were formed and broken between particles, based on their interaction strengths. During the process, a new simulation environment based on Newtonian mechanics and elementary interactions between the particles was created, and a new method for evaluating mixing was developed. Powder behavior is a complicated process, and many of its aspects are still unclear. Powders as a whole exhibit some aspects of solids and others of liquids. Therefore, their physics is far from clear. However, using relatively simple models based on particle-particle interaction, many powder properties could be replicated during this work. Simulated packing densities were similar to values reported in the literature. The method developed for describing powder mixing correlated well with previous methods. The new method can be applied to determine mixing in completely homogeneous materials, without dividing them into different components. As such, it can describe the efficiency of the mixing method, regardless of the powder's initial setup. The mixing efficiency at different vibrations was examined, and we found that certain combinations of amplitude, direction, and frequencies resulted in better mixing while using less energy. Simulations using exponential force potentials between particles were able to explain the elementary compression behavior of tablets, and create force distributions that were similar to the pressure distributions reported in the literature. Tablet-breaking simulations resulted in breaking strengths that were similar to measured tablet breaking strengths. In general, many aspects of powder behavior can be explained with mechanical interactions at the particle level, and single particle properties can be reliably linked to powder behavior with accurate simulations.