Adhesion,Presence and Antifouling of Deinococcus geothermalis in Paper Machine Environment

This thesis has two items: biofouling and antifouling in paper industry. Biofouling means unwanted microbial accumulation on surfaces causing e.g. disturbances in industrial processes, contamination of medical devices or of water distribution networks. Antifouling focuses on preventing accumulation of the biofilms in undesired places. Deinococcus geothermalis is a pink-pigmented, thermophilic bacterium, and extremely resistant towards radiation, UV-light and desiccation and known as a biofouler of paper machines forming firm and biocide resistant biofilms on the stainless steel surfaces. The compact structure of biofilm microcolonies of D. geothermalis E50051 and the adhesion into abiotic surfaces were investigated by confocal laser scanning microscope combined with carbohydrate specific fluorescently labelled lectins. The extracellular polymeric substance in D. geothermalis microcolonies was found to be a composite of at least five different glycoconjugates contributing to adhesion, functioning as structural elements, putative storages for water, gliding motility and likely also to protection. The adhesion threads that D. geothermalis seems to use to adhere on an abiotic surface and to anchor itself to the neighbouring cells were shown to be protein. Four protein components of type IV pilin were identified. In addition, the lectin staining showed that the adhesion threads were covered with galactose containing glycoconjugates. The threads were not exposed on planktic cells indicating their primary role in adhesion and in biofilm formation. I investigated by quantitative real-time PCR the presence of D. geothermalis in biofilms, deposits, process waters and paper end products from 24 paper and board mills. The primers designed for doing this were targeted to the 16S rRNA gene of D. geothermalis. We found D. geothermalis DNA from 9 machines, in total 16 samples of the 120 mill samples searched for. The total bacterial content varied in those samples between 107 to 3 ×1010 16S rRNA gene copies g-1. The proportion of D. geothermalis in those same samples was minor, 0.03 1.3 % of the total bacterial content. Nevertheless D. geothermalis may endanger paper quality as its DNA was shown in an end product. As an antifouling method towards biofilms we studied the electrochemical polarization. Two novel instruments were designed for this work. The double biofilm analyzer was designed for search for a polarization program that would eradicate D. geothermalis biofilm or from stainless steel under conditions simulating paper mill environment. The Radbox instrument was designed to study the generation of reactive oxygen species during the polarization that was effective in antifouling of D. geothermalis. We found that cathodic character and a pulsed mode of polarization were required to achieve detaching D. geothermalis biofilm from stainless steel. We also found that the efficiency of polarization was good on submerged, and poor on splash area biofilms. By adding oxidative biocides, bromochloro-5,5-dimethylhydantoin, 2,2-dibromo-2-cyanodiacetamide or peracetic acid gave additive value with polarization, being active on splash area biofilms. We showed that the cathodically weighted pulsed polarization that was active in removing D. geothermalis was also effective in generation of reactive oxygen species. It is possible that the antifouling effect relied on the generation of ROS on the polarized steel surfaces. Antifouling method successful towards D. geothermalis that is a tenacious biofouler and possesses a high tolerance to oxidative stressors could be functional also towards other biofoulers and applicable in wet industrial processes elsewhere.

Primary structure of belladonna mottle virus coat protein.

The coat protein of belladonna mottle virus (a tymovirus) was cleaved by trypsin and chymotrypsin, and the peptides were separated by high performance liquid chromatography using a combination of gel permeation, reverse phase, and ion pair chromatography. The peptides were sequenced manually using the 4-N, N-dimethylaminoazobenzene-4'-isothiocyanate/phenyl isothiocyanate double-coupling method. The chymotryptic peptides were aligned by overlapping sequences of tryptic peptides and by homology with another tymovirus, eggplant mosaic virus. The belladonna mottle virus is more closely related to eggplant mosaic virus than to turnip yellow mosaic virus, the type member of this group, as evident from the sequence homologies of 57 and 32%, respectively. The accumulation of basic residues at the amino terminus implicated in RNA-protein interactions in many spherical plant viruses was absent in all the three sequences. Interestingly, the amino-terminal region is the least conserved among the tymoviruses. The longest stretch of conserved sequence between belladonna mottle virus and eggplant mosaic virus was residues 34-44, whereas it was residues 96-102 in the case of belladonna mottle virus and turnip yellow mosaic virus. A tetrapeptide in the region (residues 154-157) was found to be common for all the three sequences. It is possible that these conserved regions (residues 34-44, 96-102, 154-157) are involved in either intersubunit or RNA-protein interactions.

On the use of weather radar for mesoscale applications in northern conditions

Mesoscale weather phenomena, such as the sea breeze circulation or lake effect snow bands, are typically too large to be observed at one point, yet too small to be caught in a traditional network of weather stations. Hence, the weather radar is one of the best tools for observing, analyzing and understanding their behavior and development. A weather radar network is a complex system, which has many structural and technical features to be tuned, from the location of each radar to the number of pulses averaged in the signal processing. These design parameters have no universal optimal values, but their selection depends on the nature of the weather phenomena to be monitored as well as on the applications for which the data will be used. The priorities and critical values are different for forest fire forecasting, aviation weather service or the planning of snow ploughing, to name a few radar-based applications. The main objective of the work performed within this thesis has been to combine knowledge of technical properties of the radar systems and our understanding of weather conditions in order to produce better applications able to efficiently support decision making in service duties for modern society related to weather and safety in northern conditions. When a new application is developed, it must be tested against ground truth . Two new verification approaches for radar-based hail estimates are introduced in this thesis. For mesoscale applications, finding the representative reference can be challenging since these phenomena are by definition difficult to catch with surface observations. Hence, almost any valuable information, which can be distilled from unconventional data sources such as newspapers and holiday shots is welcome. However, as important as getting data is to obtain estimates of data quality, and to judge to what extent the two disparate information sources can be compared. The presented new applications do not rely on radar data alone, but ingest information from auxiliary sources such as temperature fields. The author concludes that in the future the radar will continue to be a key source of data and information especially when used together in an effective way with other meteorological data.

Thyroidal control of hepatic release and metabolism of vitamin A

The inverse relationship that exists between thyroxine and the vitamin A level of plasma has been examined in chicken. Thyroxine treatment leads to a decrease in the level of vitamin A carrier proteins, retinol-binding protein and prealbumin-2 in plasma and liver. There is an accumulation of vitamin A in the liver, with a greater proportion of vitamin A alcohol being present compared to that of control birds. In thyroxine treatment there is enhanced plasma turnover of retinol-binding protein and prealbumin-2, while their rates of synthesis are marginally increased. Amino acid supplementation partially counteracts effects of thyroxine treatment. Amino acid supplementation of thyroxine-treated birds does not alter the plasma turnover rates of retinol-binding protein and prealbumin-2 but increases substentially their rates of synthesis. The release of vitamin A into circulation is interfered with in hyperthyroidism due to inadequate availability of retinol-binding protein being caused by enhanced plasma turnover rate not compensated for by synthesis.

Proteolytic susceptibility and methionine modification of monodeamidated ribonuclease A

The susceptibility of a monodeamidated RNAaseA (RNAaseAa1) towards carboxypeptidaseA , alpha-chymotrypsin and pepsin has been studied. Similar to RNAaseA, the C-terminal of RNAaseAa1 is not available for carboxypeptidaseA hydrolysis. The thermal stability of RNAaseAa1 as probed through chymotryptic digestion is found to be less than that of RNAaseA. Preliminary chromatographic analysis of the digested material, however, suggests that the nature of thermal transition might be the same in the two proteins. Pepsin inactivates RNAaseAa1 more slowly than does RNAaseA. Accordingly, less peptide bonds, almost half that of RNAaseA, are cleaved by pepsin in RNAaseAa1. The accumulation of RNAase-P type intermediates is not evident during peptic digestion of RNAaseAa1. Reaction with O-benzoquinone at low pH shows that methionines of the deamidated protein seem to have higher reactivities. These observations indicate a different structure for RNAaseAa1 at elevated temperature and low pH.

Generation of a Manganese Specific Restriction Endonuclease with Nicking Activity

A typical feature of type II restriction endonucleases (REases) is their obligate sequence specificity and requirement for Mg2+ during catalysis. R.KpnI is an exception. Unlike most other type II REases, the active site of this enzyme can accommodate Mg2+, Mn2+, Ca2+, or Zn2+ and cleave DNA. The enzyme belongs to the HNH superfamily of nucleases and is characterized by the presence of a beta beta alpha-Me finger motif. Residues D148, H149, and Q175 together form the HNH active site and are essential for Mg2+ binding and catalysis. The unique ability of the enzyme to cleave DNA in the presence of different metal ions is exploited to generate mutants that are specific to one particular metal ion. We describe the generation of a Mn2+-dependent sequence specific endonuclease, defective in DNA cleavage with Mg2+ and other divalent metal ions. In the engineered mutant, only Mn2+ is selectively bound at the active site, imparting Mn2+-mediated cleavage. The mutant is impaired in concerted double-stranded DNA cleavage, leading to accumulation of nicked intermediates. The nicking activity of the mutant enzyme is further enhanced by altered reaction conditions. The active site fluidity of R Eases allowing flexible accommodation of catalytic cofactors thus forms a basis for engineering selective metal ion-dependent REase additionally possessing nicking activity.

Fast- and drift-ice communities in the Bothnian Bay and the impact of UVA radiation on the Baltic Sea ice ecology

The aim of this thesis was to study ecology of Baltic Sea ice from two perspectives. In the first two studies, sea-ice ecology from riverine-influenced fast ice to drift ice in the Bothnian Bay was investigated, whereas the last two studies focus on the sensitivity of sea-ice bacteria and algae to UVA examined in situ. The seasonal sea ice cover is one of the main characteristics of the Baltic Sea, and despite the brackish parental water, the ice structure is similar to polar ice with saline brine inclusions, the sea ice habitat. The decreasing seawater salinity from the northern Baltic Sea to the Bothnian Bay translates to decreasing brine volumes along the gradient, governing the size and community structure of the food webs in ice. However, the drift and fast ice in the Bothnian Bay may differ greatly in this sense, as drift ice may have been formed at more southern locations. Rafting and the formation of snow ice are common processes in the ice field of the Bothnian Bay. As evidenced in this thesis, rafting altered the vertical distribution of organisms and snow-ice formation provided habitable space in the better-illuminated, nitrogen-rich surface layer. The divergence between fast and drift ice became apparent at the more advanced stages, and chlorophyte biomass decreased from fast to drift ice, while the opposite held true for protozoan and metazoan biomass. The brine volumes affected the communities somewhat, and a higher percentage of flagellate species was generally linked to lower brine volumes, whereas chain-forming diatoms were mostly concentrated in layers with larger brine volumes. These results add to knowledge of the ecological significance of the ice cover lasting up to 7 months per year in this area. Sea-ice food webs are generally light-limited, but while increasing light irradiances typically enhance the primary production and further, the secondary production in sea ice, any increase in solar radiation also includes an increase in harmful UVA radiation. The Baltic Sea ice microbial communities were clearly sensitive to UVA and the responses were strongly linked to the earlier light history, as well as to the solar irradiances they were exposed to. The increased biomass of chlorophytes and pennate diatoms, when UVA was excluded, indicates that their normally minor contribution to the biomass in the upper layers of sea ice might be partly dictated by UVA. The effects of UVA on bacterial production in Baltic Sea ice mostly followed the responses in algal growth, but occasionally the exposure to UVA even enhanced the bacterial production. The dominant bacterial class, Flavobacteria, seemed to be UVA-tolerant, whereas all the Alpha-, Beta- and Gammaproteobacteria present in the surface layer showed UVA sensitivity. These results indicate that changes in the light field of ice may alter the community structure and affect the functioning of ice food webs, and are of importance when the effects of thinning of the ice cover are assessed.

Effect of Neutralization of Endogenous Follicle Stimulating Hormone (FSH) or Luteinizing Hormone (LH) on Ovarian Lipids in the Hamster: A Histochemical and Biochemical Evaluation

The effect of neutralizing FSH or LH on ovarian lipids in the cycling hamster was studied. In the normal cycling hamster on the day of proestrus, histochemical examination revealed the presence of sudanophilic lipids in the granulosa cells of the follicles and in the interstitium. A clear reduction in the intensity of lipid staining was observed on proestrus in the ovary of hamsters treated with FSH antiserum on the previous proestrus. Similar treatment with antiserum to LH, on the other hand, caused an accumulation of lipids in these structures. Estimation of the free and esterified fractions of cholesterol and triglycerides in the nonluteal tissue of the ovary of hamsters on proestrus following treatment with FSH antiserum on the previous proestrus revealed a significant reduction in all 3 lipid components. Even a short term deprivation of FSH caused a similar reduction in these lipids in the ovary. In contrast, treatment with LH antiserum either on the previous proestrus or on the previous day (diestrus-2) resulted in an enhancement in esterified cholesterol and triglycerides, while it caused a reduction in the free cholesterol fraction of the ovary on proestrus.It is suggested that though treatment with antisera to either FSH or LH causes a disruption in follicular maturation, their effect on lipid metabolism is different. A positive role for FSH and LH in maintaining normal sterol and triglyceride levels in the nonluteal ovarian tissue of cycling hamster is indicated.

Development stage-specific expression of fibroin in the silk worm Bombyx mori is regulated translationally

The contents of fibroin H RNA as a function of development have been quantitated in the posterior silk glands of Bombyx mori larvae on different days of 4th and 5th instars. The fibroin RNA levels increased during the feeding stages of larvae and the RNA got completely degraded during the interim moult. The patterns of accumulation of fibroin RNA were similar in both the instars. Although there was considerable increase in the fibroin RNA content during the 5th larval instar, the relative abundance of fibroin RNA in the total RNA was fairly constant during the 4th and 5th instars. The increased content of fibroin RNA in 5th instar was the consequence of an overall increase in transcription accompanying the development progress, rather than specific increase only in fibroin transcription. The contents of fibroin protein in the 4th and 5th instars of development have also been quantitated making use of a sensitive radioimmune assay with a purified, antifibroin antibody. There were substantial differences between 4th and 5th instars in the absolute fibroin contents as well as the relative proportion of fibroin in the total proteins. These results implied that although the fibroin gene was transcribed at the same efficiency during the 4th and 5th instars, the translational efficiency was much lower during the 4th instar. The extent of polyadenylation of fibroin RNA was similar in both instars. However, there was a two-fold increase in the polysome association of fibroin RNA in the 5th instar. Over and above this, there was substantial increase during the 5th instar in the contents of those tRNAs. (e.g. Gly, Ala and Ser) which are abundantly represented in fibroin and therefore directly related to the expression of fibroin. The increased polysome association of fibroin mRNA and the adequate supply of cognate tRNAs in the 5th instar, together contributes to the translational regulation of fibroin in a developmental stage-specific manner. Based on these observations, we propose that translational regulation plays a major role in the development stage-specific synthesis of fibroin in Bombyx mori.

Functional expression and subcellular localization of the Cl- cotransporters KCC2 and NKCC1 in rodent hippocampal and neocortical neurons

The work presented here has focused on the role of cation-chloride cotransporters (CCCs) in (1) the regulation of intracellular chloride concentration within postsynaptic neurons and (2) on the consequent effects on the actions of the neurotransmitter gamma-aminobutyric acid (GABA) mediated by GABAA receptors (GABAARs) during development and in pathophysiological conditions such as epilepsy. In addition, (3) we found that a member of the CCC family, the K-Cl cotransporter isoform 2 (KCC2), has a structural role in the development of dendritic spines during the differentiation of pyramidal neurons. Despite the large number of publications dedicated to regulation of intracellular Cl-, our understanding of the underlying mechanisms is not complete. Experiments on GABA actions under resting steady-state have shown that the effect of GABA shifts from depolarizing to hyperpolarizing during maturation of cortical neurons. However, it remains unclear, whether conclusions from these steady-state measurements can be extrapolated to the highly dynamic situation within an intact and active neuronal network. Indeed, GABAergic signaling in active neuronal networks results in a continuous Cl- load, which must be constantly removed by efficient Cl- extrusion mechanisms. Therefore, it seems plausible to suggest that key parameters are the efficacy and subcellular distribution of Cl- transporters rather than the polarity of steady-state GABA actions. A further related question is: what are the mechanisms of Cl- regulation and homeostasis during pathophysiological conditions such as epilepsy in adults and neonates? Here I present results that were obtained by means of a newly developed method of measurements of the efficacy of a K-Cl cotransport. In Study I, the developmental profile of KCC2 functionality during development was analyzed both in dissociated neuronal cultures and in acute hippocampal slices. A novel method of photolysis of caged GABA in combination with Cl- loading to the somata was used in this study to assess the extrusion efficacy of KCC2. We demonstrated that these two preparations exhibit a different temporal profile of functional KCC2 upregulation. In Study II, we reported an observation of highly distorted dendritic spines in neurons cultured from KCC2-/- embryos. During their development in the culture dish, KCC2-lacking neurons failed to develop mature, mushroom-shaped dendritic spines but instead maintained an immature phenotype of long, branching and extremely motile protrusions. It was shown that the role of KCC2 in spine maturation is not based on its transport activity, but is mediated by interactions with cytoskeletal proteins. Another important player in Cl- regulation, NKCC1 and its role in the induction and maintenance of native Cl- gradients between the axon initial segment (AIS) and soma was the subject of Study III. There we demonstrated that this transporter mediates accumulation of Cl- in the axon initial segment of neocortical and hippocampal principal neurons. The results suggest that the reversal potential of the GABAA response triggered by distinct populations of interneurons show large subcellular variations. Finally, a novel mechanism of fast post-translational upregulation of the membrane-inserted, functionally active KCC2 pool during in-vivo neonatal seizures and epileptiform-like activity in vitro was identified and characterized in Study IV. The seizure-induced KCC2 upregulation may act as an intrinsic antiepileptogenic mechanism.

Sensitivity of the simulated precipitation to changes in convective relaxation time scale

The paper describes the sensitivity of the simulated precipitation to changes in convective relaxation time scale (TAU) of Zhang and McFarlane (ZM) cumulus parameterization, in NCAR-Community Atmosphere Model version 3 (CAM3). In the default configuration of the model, the prescribed value of TAU, a characteristic time scale with which convective available potential energy (CAPE) is removed at an exponential rate by convection, is assumed to be 1 h. However, some recent observational findings suggest that, it is larger by around one order of magnitude. In order to explore the sensitivity of the model simulation to TAU, two model frameworks have been used, namely, aqua-planet and actual-planet configurations. Numerical integrations have been carried out by using different values of TAU, and its effect on simulated precipitation has been analyzed. The aqua-planet simulations reveal that when TAU increases, rate of deep convective precipitation (DCP) decreases and this leads to an accumulation of convective instability in the atmosphere. Consequently, the moisture content in the lower-and mid-troposphere increases. On the other hand, the shallow convective precipitation (SCP) and large-scale precipitation (LSP) intensify, predominantly the SCP, and thus capping the accumulation of convective instability in the atmosphere. The total precipitation (TP) remains approximately constant, but the proportion of the three components changes significantly, which in turn alters the vertical distribution of total precipitation production. The vertical structure of moist heating changes from a vertically extended profile to a bottom heavy profile, with the increase of TAU. Altitude of the maximum vertical velocity shifts from upper troposphere to lower troposphere. Similar response was seen in the actual-planet simulations. With an increase in TAU from 1 h to 8 h, there was a significant improvement in the simulation of the seasonal mean precipitation. The fraction of deep convective precipitation was in much better agreement with satellite observations.

Sedimentary zooplankton remains as indicators of lake ecological quality and trophic structure

To protect and restore lake ecosystems under threats posed by the increasing human population, information on their ecological quality is needed. Lake sediments provide a data rich archive that allows identification of various biological components present prior to anthropogenic alterations as well as a constant record of changes. By providing a longer dimension of time than any ongoing monitoring programme, palaeolimnological methods can help in understanding natural variability and long-term ecological changes in lakes. As zooplankton have a central role in the lake food web, their remains can potentially provide versatile information on past trophic structure. However, various taphonomic processes operating in the lakes still raise questions concerning how subfossil assemblages reflect living communities. This thesis work aimed at improving the use of sedimentary zooplankton remains in the reconstruction of past zooplankton communities and the trophic structure in lakes. To quantify interspecific differences in the accumulation of remains, the subfossils of nine pelagic zooplankton taxa in annually laminated sediments were compared with monitoring results for live zooplankton in Lake Vesijärvi. This lake has a known history of eutrophication and recovery, which resulted from reduced external loading and effective fishing of plankti-benthivorous fish. The response of zooplankton assemblages to these known changes was resolved using annually laminated sediments. The generality of the responses observed in Lake Vesijärvi were further tested with a set of 31 lakes in Southern Finland, relating subfossils in surface sediments to contemporary water quality and fish density, as well as to lake morphometry. The results demonstrated differential preservation and retention of cladoceran species in the sediment. Daphnia, Diaphanosoma and Ceriodaphnia were clearly underrepresented in the sediment samples in comparison to well-preserved Bosmina species, Chydorus, Limnosida and Leptodora. For well-preserved species, the annual net accumulation rate was similar to or above the expected values, reflecting effective sediment focusing and accumulation in the deepest part of the lake. The decreased fish density and improved water quality led to subtle changes in zooplankton community composition. The abundance of Diaphanosoma and Limnosida increased after the reduction in fish density, while Ceriodaphnia and rotifers decreased. The most sensitive indicator of fish density was the mean size of Daphnia ephippia and Bosmina (E.) crassicornis ephippia and carapaces. The concentration of plant-associated species increased, reflecting expanding littoral vegetation along with increasing transparency. Several of the patterns observed in Lake Vesijärvi could also be found within the set of 31 lakes. According to this thesis work, the most useful cladoceran-based indices for nutrient status and planktivorous fish density in Finnish lakes were the relative abundances of certain pelagic taxa, and the mean size of Bosmina spp. carapaces, especially those of Bosmina (E.) cf. coregoni. The abundance of plant-associated species reflected the potential area for aquatic plants. Lake morphometry and sediment organic content, however, explained a relatively high proportion of the variance in the species data, and more studies are needed to quantify lake-specific differences in the accumulation and preservation of remains. Commonly occurring multicollinearity between environmental variables obstructs the cladoceran-based reconstruction of single environmental variables. As taphonomic factors and several direct and indirect structuring forces in lake ecosystems simultaneously affect zooplankton, the subfossil assemblages should be studied in a holistic way before making final conclusions about the trophic structure and the change in lake ecological quality.

devovo biosynthesis of heme offers a new chemotherapeutic target in the human malarial parasite

The human malarial parasite, Image , has been found to synthesize heme Image , despite the accumulation of large quantities of polymeric heme derived from the hemoglobin of the red cell host. The parasite δ-aminolevulinate dehydrase level is significantly lower than that of the host and its inhibition by succinylacetone leads to inhibition of parasite protein synthesis and viability.

Involvement of Cytochrome P450 in Conferring Chloroquine Resistance to the Malarial Parasite, Plasmodium falciparum

The higher levels of cytochrone P-450 dependent enzyme activities reported earlier are traced to higher levels of cytochrome P-450 (CYPIIB1/B2 like) messenger RNA in the chloroquine resistant than the sensitive strains. The messenger RNA is also induced by phenobarbitone in the sensitive strain. Pretreatment with phenobarbitone affords partial protection to chloroquine toxicity in the sensitive strain and this is not due to a differential accumulation of the drug.

Purification and characterization of an extracellular β-glucosidase from the thermophilic fungus Sporotrichum thermophile and its influence on cellulase activity

Multiple forms of beta-glucosidase (EC 3.2.1.21) of Sporotrichum thermophile were produced when the fungus was grown in a cellulose medium. One beta-glucosidase was purified 16-fold from 6-d-old culture filtrates by ion-exchange and gel-filtration chromatography. The purified enzyme was free of cellulase activity. It hydrolysed aryl beta-D-glucosides and beta-D-linked diglucosides. It was optimally active at pH 5.4, at 65-degrees-C. The apparent K(m) values for p-nitrophenyl beta-D-glucoside (PNPG) and cellobiose were 0.29 and 0.83 mm, respectively. Glucose, fucose, nojirimycin and gluconolactone inhibited beta-glucosidase competitively. At high (> 1 mm) substrate concentration, beta-glucosidase catalysed a parallel transglycosylation reaction. The transglycosylation product formed from cellobiose appeared to be a beta-linked tetramer of glucose. Admixtures of beta-glucosidase and cellulase components showed that the concept of cellobiose inhibition of cellulases was not valid for all components of the cellulase system of S. thermophile. Beta-Glucosidase supplementation also stimulated cellulose hydrolysis by cellulases when there was no accumulation of cellobiose in reaction mixture.