Shwachman-Diamond syndrome : Clinical, genetic and radiological study

Shwachman-Diamond syndrome (SDS) is a rare autosomal recessive disorder in which the cardinal symptoms arise from exocrine pancreatic insufficiency and bone marrow dysfunction. Previous studies have suggested increased risk of fatal complications among Finnish SDS infants. The genetic defect responsible for the disease was recently identified; the SBDS gene is located at chromosome 7q11 and encodes a protein that is involved in ribosome biosynthesis. The discovery of the SBDS gene has opened new insights into the pathogenesis of this multi-organ disease. This study aimed to assess phenotypic and genotypic features of Finnish patients with SDS. Seventeen Finnish patients with a clinical diagnosis of SDS were included in the study cohort. Extensive clinical, biochemical and imaging assessments were performed to elucidate the phenotypic features, and the findings were correlated with the SBDS genotype. Imaging studies included abdominal magnetic reso-nance imaging (MRI), brain MRI, cardiac echocardiography including tissue Doppler examination, and cardiac MRI. The skeletal phenotype was assessed by dual-energy X-ray absorptiometry and bone histomorphometry. Twelve patients had mutations in the SBDS gene. In MRI, a characteristic pattern of fat-replaced pancreas with occasional enhancement of scattered parenchymal foci and of pancreatic duct was noted in the SBDS mutation-positive patients while the mutation-negative patients did not have pancreatic fat accumulation. The patients with SBDS mutations had significantly reduced bone mineral density associated with low-energy peripheral fractures and vertebral compression fractures. Bone histomorphometry confirmed low-turnover osteoporosis. The patients with SBDS mutations had learning difficulties and smaller head size and brain volume than control subjects. Corpus callosum, cerebellar vermis, and pos-terior fossa structures were significantly smaller in SDS patients than in controls. Patients with SDS did not have evidence of clinical heart disease or myocardial fibrosis. However, subtle diastolic changes in the right ventricle and exercise-induced changes in the left ventricle contractile reserve were observed. This study expanded the phenotypic features of SDS to include primary low-turnover osteoporosis and structural alterations in the brain. Pancreatic MRI showed characteristic changes in the SBDS mutation-positive patients while these were absent in the mutation-negative patients, suggesting that MRI can be used to differentiate patients harbouring SBDS mutations from those without mutations. No evidence for clinical cardiac manifestations was found, but imaging studies revealed slightly altered myocardial function that may have clinical implications. These findings confirm the pleiotropic nature of SDS and underscore the importance of careful multidisciplinary follow-up of the affected individuals.

Lifting the singular nature of a model for peeling of an adhesive tape

We investigate the dynamics of peeling of an adhesive tape subjected to a constant pull speed. Due to the constraint between the pull force, peel angle and the peel force, the equations of motion derived earlier fall into the category of differential-algebraic equations (DAE) requiring an appropriate algorithm for its numerical solution. By including the kinetic energy arising from the stretched part of the tape in the Lagrangian, we derive equations of motion that support stick-slip jumps as a natural consequence of the inherent dynamics itself, thus circumventing the need to use any special algorithm. In the low mass limit, these equations reproduce solutions obtained using a differential-algebraic algorithm introduced for the earlier singular equations. We find that mass has a strong influence on the dynamics of the model rendering periodic solutions to chaotic and vice versa. Apart from the rich dynamics, the model reproduces several qualitative features of the different waveforms of the peel force function as also the decreasing nature of force drop magnitudes.

Rheology of dense sheared granular flows

Rapid granular flows are defined as flows in which the time scales for the particle interactions are small compared to the inverse of the strain rate, so that the particle interactions can be treated as instantaneous collisions. We first show, using Discrete Element simulations, that even very dense flows of sand or glass beads with volume fraction between 0.5 and 0.6 are rapid granular flows. Since collisions are instantaneous, a kinetic theory approach for the constitutive relations is most appropriate, and we present kinetic theory results for different microscopic models for particle interaction. The significant difference between granular flows and normal fluids is that energy is not conserved in a granular flow. The differences in the hydrodynamic modes caused by the non-conserved nature of energy are discussed. Going beyond the Boltzmann equation, the effect of correlations is studied using the ring kinetic approximation, and it is shown that the divergences in the viscometric coefficients, which are present for elastic fluids, are not present for granular flows because energy is not conserved. The hydrodynamic model is applied to the flow down an inclined plane. Since energy is not a conserved variable, the hydrodynamic fields in the bulk of a granular flow are obtained from the mass and momentum conservation equations alone. Energy becomes a relevant variable only in thin 'boundary layers' at the boundaries of the flow where there is a balance between the rates of conduction and dissipation. We show that such a hydrodynamic model can predict the salient features of a chute flow, including the flow initiation when the angle of inclination is increased above the 'friction angle', the striking lack of observable variation of the volume fraction with height, the observation of a steady flow only for certain restitution coefficients, and the density variations in the boundary layers.

Dynamic nature of proteins - interpretation of residual dipolar couplings

Protein conformations and dynamics can be studied by nuclear magnetic resonance spectroscopy using dilute liquid crystalline samples. This work clarifies the interpretation of residual dipolar coupling data yielded by the experiments. It was discovered that unfolded proteins without any additional structure beyond that of a mere polypeptide chain exhibit residual dipolar couplings. Also, it was found that molecular dynamics induce fluctuations in the molecular alignment and doing so affect residual dipolar couplings. The finding clarified the origins of low order parameter values observed earlier. The work required the development of new analytical and computational methods for the prediction of intrinsic residual dipolar coupling profiles for unfolded proteins. The presented characteristic chain model is able to reproduce the general trend of experimental residual dipolar couplings for denatured proteins. The details of experimental residual dipolar coupling profiles are beyond the analytical model, but improvements are proposed to achieve greater accuracy. A computational method for rapid prediction of unfolded protein residual dipolar couplings was also developed. Protein dynamics were shown to modulate the effective molecular alignment in a dilute liquid crystalline medium. The effects were investigated from experimental and molecular dynamics generated conformational ensembles of folded proteins. It was noted that dynamics induced alignment is significant especially for the interpretation of molecular dynamics in small, globular proteins. A method of correction was presented. Residual dipolar couplings offer an attractive possibility for the direct observation of protein conformational preferences and dynamics. The presented models and methods of analysis provide significant advances in the interpretation of residual dipolar coupling data from proteins.

Mathematics, nature and cryptography: Insights from philosophy of information

One influential image that is popular among scientists is the view that mathematics is the language of nature. The present article discusses another possible way to approach the relation between mathematics and nature, which is by using the idea of information and the conceptual vocabulary of cryptography. This approach allows us to understand the possibility that secrets of nature need not be written in mathematics and yet mathematics is necessary as a cryptographic key to unlock these secrets. Various advantages of such a view are described in this article.

The Rocky Road of Social Sustainability : The Impact of Integrated Biodiversity Conservation and Development on the Local Realities in Ranomafana National Park, Madagascar

The objective of this study is to examine the social impacts of the integrated conservation and development project (ICDP) aimed at biodiversity conservation and local socio-economic development in the Ranomafana National Park (RNP), Madagascar. Furthermore, the study explores social sustainability and justice of the ICDP in Ranomafana. This ethnographically informed impact study uses of various field methods. The research material used consists of observation, interviews (key-person and focus group), school children's writings, official statistics and project documents. Fieldwork was conducted in three phases in 2001, 2002 and 2004 in twelve villages around the park, as well as in neighbouring areas of Ranomafana. However, four of those twelve villages were chosen for closer study. This study consists of five independent articles and a concluding chapter. Social impacts were studied through reproductive health indicators as well as a life security approach. Equity and distribution of benefits and drawbacks of ICDP were analysed and the actors related to the conservation in Ranomafana were identified. The children and adolescents' environmental views were also examined. The reproductive health indicators studied showed a poor state of reproductive health in the park area. Moreover, the existing social capital in the villages seemed to be fragmented due to economic difficulties that were partly caused by the conservation regulations. The ICDP in Ranomafana did not pay attention to the heterogeneity of the affected communities even though the local beneficiaries of the ICDP varied according to their ethnicity, living place, wealth, social position and gender. In addition, various conservation actors (local people in various groups, local authorities, tourist business owners, conservation NGOs and scientists) contest their interests over the forest, conservation and its related activities. This study corroborates the same type of evidence and conclusions discussed in other similar cases elsewhere: so called social conservation programmes still cannot meet the needs of the people living near the protected areas; on the contrary, they even have a reverse impact on the people's lives. A fundamental misunderstood assumption in the conservation process in Ranomafana was to consider the local people as a problem for biodiversity conservation. Major reasons for the failure of the ICDP in Ranomafana include a lack of local institutions that would have been able to communicate as equals with the conservation NGOs as well as to transfer the tradition of the authoritarian governance in conservation management together with the over-appreciation of scientific biodiversity, and lack of will to understand the local people's rights to use the forest for their livelihoods.

Disallowed Ramachandran Conformations of Amino Acid Residues in Protein Structures

An analysis of the nature and distribution of disallowed Ramachandran conformations of amino acid residues observed in high resolution protein crystal structures has been carried out. A data set consisting of 110 high resolution, non-homologous, protein crystal structures from the Brookhaven Protein Data Bank was examined. The data set consisted of a total of 18,708 non-Gly residues, which were characterized on the basis of their backbone dihedral angles (φ, ψ). Residues falling outside the defined “broad allowed limits” on the Ramachandran map were chosen and the reportedB-factor value of the α-carbon atom was used to further select well defined disallowed conformations. The conformations of the selected 66 disallowed residues clustered in distinct regions of the Ramachandran map indicating that specific φ, ψ angle distortions are preferred under compulsions imposed by local constraints. The distribution of various amino acid residues in the disallowed residue data set showed a predominance of small polar/charged residues, with bulky hydrophobic residues being infrequent. As a further check, for all the 66 cases non-hydrogen van der Waals short contacts in the protein structures were evaluated and compared with the ideal “Ala-dipeptide” constructed using disallowed dihedral angle (φ, ψ) values. The analysis reveals that short contacts are eliminated in most cases by local distortions of bond angles. An analysis of the conformation of the identified disallowed residues in related protein structures reveals instances of conservation of unusual stereochemistry.

Group Beliefs : Studies on the Nature and Logic of Collective Doxastic Attitudes

This thesis studies the nature and logic of collective doxastic attitudes, or what is referred to in ordinary language as "group beliefs". Beliefs and other intentional attitudes are attributed to groups and collections of people, and such attributions are used to explain and predict the actions of groups. The thesis develops an understanding of group beliefs as voluntarily adopted views or acceptances rather than as ordinary beliefs. Such an understanding can provide new answers to questions concerning collective knowledge and justification of group beliefs, and it allows developing modal logics with collective doxastic and epistemic notions. The thesis consists of six articles. The first three articles are philosophical studies concerned with the nature of group beliefs. The last three articles are logical studies that aim at developing proof-theoretical calculi for reasoning about collective doxastic attitudes.

Evolutionary and conservation biology of the Finnish house sparrow

Recently it has been recognized that evolutionary aspects play a major role in conservation issues of a species. In this thesis I have combined evolutionary research with conservation studies to provide new insight into these fields. The study object of this thesis is the house sparrow, a species that has features that makes it interesting for this type of study. The house sparrow has been ubiquitous almost all over the world. Even though being still abundant, several countries have reported major declines. These declines have taken place in a relatively short time covering both urban and rural habitats. In Finland this species has declined by more than two thirds in just over two decades. In addition, as the house sparrow lives only in human inhabited areas it can also raise public awareness to conservation issues. I used both an extensive museum collection of house sparrows collected in 1980s from all over Finland as well as samples collected in 2009 from 12 of the previously collected localities. I used molecular techniques to study neutral genetic variation within and genetic differentiation between the study populations. This knowledge I then combined with data gathered on morphometric measurements. In addition I analyzed eight heavy metals from the livers of house sparrows that lived in either rural or urban areas in the 1980s and evaluated the role of heavy metal pollution as a possible cause of the declines. Even though dispersal of house sparrows is limited I found that just as the declines started in 1980s the house sparrows formed a genetically panmictic population on the scale of the whole Finland. When compared to Norway, where neutral genetic divergence has been found even with small geographic distances, I concluded that this difference would be due to contrasting landscapes. In Finland the landscape is rather homogeneous facilitating the movements of these birds and maintaining gene flow even with the low dispersal. To see whether the declines have had an effect on the neutral genetic variation of the populations I did a comparison between the historical and contemporary genetic data. I showed that even though genetic diversity has not decreased due to the drastic declines the populations have indeed become more differentiated from each other. This shows that even in a still quite abundant species the declines can have an effect on the genetic variation. It is shown that genetic diversity and differentiation may approach their new equilibriums at different rates. This emphasizes the importance of studying both of them and if the latter has increased it should be taken as a warning sign of a possible loss of genetic diversity in the future. One of the factors suggested to be responsible for the house sparrow declines is heavy metal pollution. When studying the livers of house sparrows from 1980s I discovered higher levels of heavy metal concentrations in urban than rural habitats, but the levels of the metals were comparatively low and based on that heavy metal pollution does not seem to be a direct cause for the declines in Finland. However, heavy metals are known to decrease the amount of insects in urban areas and thus in the cities heavy metals may have an indirect effect on house sparrows. Although neutral genetic variation is an important tool for conservation genetics it does not tell the whole story. Since neutral genetic variation is not affected by selection, information can be one-sided. It is possible that even neutral genetic differentiation is low, there can be substantial variation in additive genetic traits indicating local adaptation. Therefore I performed a comparison between neutral genetic differentiation and phenotypic differentiation. I discovered that two traits out of seven are likely to be under directional selection, whereas the others could be affected by random genetic drift. Bergmann s rule may be behind the observed directional selection in wing length and body mass. These results highlight the importance of estimating both neutral and adaptive genetic variation.

Nature, stability and bonding of the peroxy group in peroxy titanium compounds

Some physicochemical properties of peroxy titanium compounds are explained by assigning a strained triangular ring structure to the peroxy titanyl group, with a bent and reduced overlap of the O---O bonding orbitals. The stability of the peroxy group is found to depend on the stability of the other ligands. The decreasing order of stability of the peroxy group in the compounds is as: oxalato > meleato > malonato > sulphato > peroxide of titanium.

Indoleacetaldoxime hydro-lyase (4.2.1.29). III. Further studies on the nature and mode of action of the enzyme

Further purification of indoleacetaldoxime (IAOX) hydro-lyase from Gibberella fujikuroi by DEAE-cellulose chromatography is described. The purified enzyme was activated by dehydroascorbic acid (DHA), ascorbic acid (AA), and pyridoxal phosphate (PALP) and was inhibited by thiol compounds and thiol reagents including phenylthiocyanate. Ferrous ions but not ferric ions activated the purified enzyme. The enzyme was activated by dihydrofolic acid but inhibited by tetrahydrofolic acid. Phenylacetaldoxime, a competitive inhibitor, afforded partial protection of the enzyme from the action of N-ethylmaleimide suggesting the involvement of a thiol function at the active site or substrate-binding site. The inhibition of the enzyme by 2,3-dimercaptopropanol was reversed by DHA, PALP, or frozen storage. KCN inhibition of the enzyme was reversed by PALP. NaBH4 reduction of the purified enzyme in the presence of PALP gave an active enzyme which was further activated by PALP or DHA but not by ferrous ions. These results suggested a "structural" role for PALP in the activity of IAOX hydro-lyase. Dilute solutions of the purified enzyme, obtained during DEAE-cellulose chromatography and concentrated using sucrose, showed enhanced activity upon frozen storage and thawing. The increase in activity of the enzyme during certain culture conditions, the activation and inhibition of the enzyme by several unrelated compounds, and the effect of freezing indicate that IAOX hydro-lyase is probably a metabolically regulated enzyme with a structure composed of subunits.

Evolution, Homology Conservation, and Identification of Unique Sequence Signatures in GH19 Family Chitinases

The discovery of GH (Glycoside Hydrolase) 19 chitinases in Streptomyces sp. raises the possibility of the presence of these proteins in other bacterial species, since they were initially thought to be confined to higher plants. The present study mainly concentrates on the phylogenetic distribution and homology conservation in GH19 family chitinases. Extensive database searches are performed to identify the presence of GH19 family chitinases in the three major super kingdoms of life. Multiple sequence alignment of all the identified GH19 chitinase family members resulted in the identification of globally conserved residues. We further identified conserved sequence motifs across the major sub groups within the family. Estimation of evolutionary distance between the various bacterial and plant chitinases are carried out to better understand the pattern of evolution. Our study also supports the horizontal gene transfer theory, which states that GH19 chitinase genes are transferred from higher plants to bacteria. Further, the present study sheds light on the phylogenetic distribution and identifies unique sequence signatures that define GH19 chitinase family of proteins. The identified motifs could be used as markers to delineate uncharacterized GH19 family chitinases. The estimation of evolutionary distance between chitinase identified in plants and bacteria shows that the flowering plants are more related to chitinase in actinobacteria than that of identified in purple bacteria. We propose a model to elucidate the natural history of GH19 family chitinases.