Microbial identification by detection of ligation probes on DNA microarray

Microbes in natural and artificial environments as well as in the human body are a key part of the functional properties of these complex systems. The presence or absence of certain microbial taxa is a correlate of functional status like risk of disease or course of metabolic processes of a microbial community. As microbes are highly diverse and mostly notcultivable, molecular markers like gene sequences are a potential basis for detection and identification of key types. The goal of this thesis was to study molecular methods for identification of microbial DNA in order to develop a tool for analysis of environmental and clinical DNA samples. Particular emphasis was placed on specificity of detection which is a major challenge when analyzing complex microbial communities. The approach taken in this study was the application and optimization of enzymatic ligation of DNA probes coupled with microarray read-out for high-throughput microbial profiling. The results show that fungal phylotypes and human papillomavirus genotypes could be accurately identified from pools of PCR amplicons generated from purified sample DNA. Approximately 1 ng/μl of sample DNA was needed for representative PCR amplification as measured by comparisons between clone sequencing and microarray. A minimum of 0,25 amol/μl of PCR amplicons was detectable from amongst 5 ng/μl of background DNA, suggesting that the detection limit of the test comprising of ligation reaction followed by microarray read-out was approximately 0,04%. Detection from sample DNA directly was shown to be feasible with probes forming a circular molecule upon ligation followed by PCR amplification of the probe. In this approach, the minimum detectable relative amount of target genome was found to be 1% of all genomes in the sample as estimated from 454 deep sequencing results. Signal-to-noise of contact printed microarrays could be improved by using an internal microarray hybridization control oligonucleotide probe together with a computational algorithm. The algorithm was based on identification of a bias in the microarray data and correction of the bias as shown by simulated and real data. The results further suggest semiquantitative detection to be possible by ligation detection, allowing estimation of target abundance in a sample. However, in practise, comprehensive sequence information of full length rRNA genes is needed to support probe design with complex samples. This study shows that DNA microarray has the potential for an accurate microbial diagnostic platform to take advantage of increasing sequence data and to replace traditional, less efficient methods that still dominate routine testing in laboratories. The data suggests that ligation reaction based microarray assay can be optimized to a degree that allows good signal-tonoise and semiquantitative detection.

Dokumentation och beskrivning som språkplanering : perspektiv från arbete med tre tecknade minoritetsspråk

Language Documentation and Description as Language Planning Working with Three Signed Minority Languages Sign languages are minority languages that typically have a low status in society. Language planning has traditionally been controlled from outside the sign-language community. Even though signed languages lack a written form, dictionaries have played an important role in language description and as tools in foreign language learning. The background to the present study on sign language documentation and description as language planning is empirical research in three dictionary projects in Finland-Swedish Sign Language, Albanian Sign Language, and Kosovar Sign Language. The study consists of an introductory article and five detailed studies which address language planning from different perspectives. The theoretical basis of the study is sociocultural linguistics. The research methods used were participant observation, interviews, focus group discussions, and document analysis. The primary research questions are the following: (1) What is the role of dictionary and lexicographic work in language planning, in research on undocumented signed language, and in relation to the language community as such? (2) What factors are particular challenges in the documentation of a sign language and should therefore be given special attention during lexicographic work? (3) Is a conventional dictionary a valid tool for describing an undocumented sign language? The results indicate that lexicographic work has a central part to play in language documentation, both as part of basic research on undocumented sign languages and for status planning. Existing dictionary work has contributed new knowledge about the languages and the language communities. The lexicographic work adds to the linguistic advocacy work done by the community itself with the aim of vitalizing the language, empowering the community, receiving governmental recognition for the language, and improving the linguistic (human) rights of the language users. The history of signed languages as low status languages has consequences for language planning and lexicography. One challenge that the study discusses is the relationship between the sign-language community and the hearing sign linguist. In order to make it possible for the community itself to take the lead in a language planning process, raising linguistic awareness within the community is crucial. The results give rise to questions of whether lexicographic work is of more importance for status planning than for corpus planning. A conventional dictionary as a tool for describing an undocumented sign language is criticised. The study discusses differences between signed and spoken/written languages that are challenging for lexicographic presentations. Alternative electronic lexicographic approaches including both lexicon and grammar are also discussed. Keywords: sign language, Finland-Swedish Sign Language, Albanian Sign Language, Kosovar Sign Language, language documentation and description, language planning, lexicography

Growth of alkali metal periodates from silica gel and their characterization

Single crystals (up to 1 cm size) of K, Rb and Cs periodates have been grown in silica gel. In general, good quality crystals were obtained in gel of specific gravity 1.04 and pH 4. The metal/iodine ratios were determined and compared with calculated values. Morphological studies were carried out using a bicircle optical goniometer. Other characterization methods include X-ray diffraction, optical absorption, differential scanning calorimetry and optical microscopy. Microscopic examination of CsIO4 crystals in particular has revealed the existence of ferroelastic domains in the crystal. The structural basis for the occurence of ferroelasticity in this crystal is discussed and the high temperature space group is predicted.

An electron diffraction study of quasicrystals in Ti-37 at% Mn and Ti-24 at% Mn-13 at% Fe alloys

Electron diffraction studies were carried out to establish the icosahedral phase formation in rapidly quenched Ti-37 at% Mn and Ti-24 at% Mn-13 at% Fe alloys. Distortions in the diffraction spots and diffuse intensities in the diffraction patterns were investigated. The existence of a rational approximant structure and a decagonal like phase are also reported.

Varistors based on n-BaTiO3 ceramics

Stable and highly reproducible voltage-limiting characteristics have been observed at room temperature for polycrystalline ceramics prepared from donor-doped BaTiO3 solid solutions containing isovalent lattice substitute ions that lower the Curie point Tc. When the ambient temperature Ta is decreased such that Ta < Tc, the same ceramics show current-limiting behaviour. The leakage current, the breakdown voltage and the non-linear coefficient (α = 30−50) could be varied with grain-boundary layer (GBL) modifiers and postsintering annealing. The magnitude of the abnormally high dielectric constant (epsilon (Porson)r greater than, approximately 105) indicates the prevalence of GBL capacitance in these ceramics. Analyses of the current-voltage relations show that GBL conduction at Ta < Tc corresponds to tunnelling across asymmetric barriers formed under steady state Joule heating. At Ta > Tc, trap-related conduction gives way to tunnelling across symmetric barriers as the field strength increases.

Glasslike elastic properties in the omega-beta alloys

We have measured the internal friction and speed of sound in several polycrystalline alloys, using compound torsional oscillators at frequencies between 60 kHz and 100 kHz and temperatures between 50 mK and 100 K. By combining these data with existing elastic and thermal data on similar alloys, we find that those alloys which can undergo diffusionsless phase transitions, such as Ti:Nb, Ti:V, or Zr:Nb in certain ranges of composition have glasslike excitations, since they have elastic properties which agree in magnitude and temperature dependence with those of amorphous solids. By contrast, crystalline continuous solution alloys, such as Nb:Ta, or alloys with diffusive phase transitions, such as high-pressure quenched Al94Si6, have the same elastic properties as are known for crystals.

Kinematic analysis and design of articulated manipulators with joint motion constraints

For an articulated manipulator with joint rotation constraints, we show that the maximum workspace is not necessarily obtained for equal link lengths but is also determined by the range and mean positions of the joint motions. We present expressions for sectional area, workspace volume, overlap volume and work area in terms of link ratios, mean positions and ranges of joint motion. We present a numerical procedure to obtain the maximum rectangular area that can be embedded in the workspace of an articulated manipulator with joint motion constraints. We demonstrate the use of analytical expressions and the numerical plots in the kinematic design of an articulated manipulator with joint rotation constraints.

Non-linear optical response of rutile-related oxides, LiM(V)M(VI)O(6), and their derivatives obtained by ion-exchange and intercalation

Polycrystalline samples of oxides of the general formula LiM(V)M(VI)O(6) (M(V) = Nb, Ta; M(VI) = Mo, W), crystallizing in a non-centrosymmetric (space group P (4) over bar 2(1)m) trirutile structure, exhibit second harmonic generation (SHG) of 1064 nm radiation with efficiencies 15-45 times that of alpha-quartz; interestingly, the SHG response is retained by the protonated derivatives HM(V)M(VI)O(6) . xH(2)O, and their n-alkylamine intercalates as well.

Thermal Stability of Spherical Nanoporous Aggregates and Formation of Hollow Structures by Sintering-A Phase-Field Study

Nanoporous structures are widely used for many applications and hence it Is important to investigate their thermal stability. We study the stability of spherical nanoporous aggregates using phase-field simulations that explore systematically the effect of grain boundary diffusion, surface diffusion, and grain boundary mobility on the pathways for microstructural evolution. Our simulations for different combinations of surface and GB diffusivity and GB mobility show four distinct microstructural pathways en route to 100% density: multiple dosed pores, hollow shells, hollow shells with a core, and multiple interconnected pores. The microstructures from our simulations are consistent with experimental observations in several different systems. Our results have important implications for rational synthesis of hollow nanostructures or aggregates with open pores, and for controlling the stability of nanoporous aggregates that are widely used for many applications.

On the decomposition of ? phase in some rapidly quenched titanium-eutectoid alloys

The decomposition of the beta phase in rapidly quenched Ti-2.8 at. pet Co, Ti-5.4 at. pet Ni, Ti-4.5 at. pet, and 5.5 at. pet Cu alloys has been investigated by electron microscopy. During rapid quenching, two competitive phase transformations, namely martensitic and eutectoid transformation, have occurred, and the region of eutectoid transformation is extended due to the high cooling rates involved. The beta phase decomposed into nonlamellar eutectoid product (bainite) having a globular morphology in Ti-2.8 pet Co and Ti-4.5 pet Cu (hypoeutectoid) alloys. In the near-eutectoid Ti-5.5 pet Cu alloy, the decomposition occurred by a lamellar (pearlite) type, whereas in Ti-5.4 pct Ni (hypereutectoid), both morphologies were observed. The interfaces between the proeutectoid alpha and the intermetallic compound in the nonlamellar type as well as between the proeutectoid alpha and the pearlite were often found to be partially coherent. These findings are in agreement with the Lee and Aaronson model proposed recently for the evolution of bainite and pearlite structures during the solid-state transformations of some titanium-eutectoid alloys. The evolution of the Ti2Cu phase during rapid quenching involved the formation of a metastable phase closely related to an ''omega-type'' phase before the equilibrium phase formed. Further, the lamellar intermetallic compound Ti2Cu was found to evolve by a sympathetic nucleation process. Evidence is established for the sympathetic nucleation of the proeutectoid alpha crystals formed during rapid quenching.

On the spurious increase in particle volume fraction during coarsening simulations

The problem of spurious increase in volume fraction of second-phase particles during computer simulations of coarsening is examined. The origin of this problem is traced to the use of too long a time step (used for numerical integration of growth rates with respect to time) which leads to small particles with large negative growth rates shrinking to negative radii at the end of the time step. Such a shrinkage to negative sizes has the effect of pumping solute into the system. It is therefore suggested that the length of the time step be chosen in accordance with the size of the smallest particle present in the system. It is shown that spurious increase in particle Volume has a significant effect on the particle size distributions in the scaling regime (making them broader and more skewed in the Lifshitz-Slyozov-Wagner model). Its effect on coarsening kinetics, however, is found to be small.

Mean field lattice model for adsorption isotherms in zeolite NaA

Using a lattice model for adsorption in microporous materials, pure component adsorption isotherms are obtained within a mean field approximation for methane at 300 K and xenon at 300 and 360 K in zeolite NaA. It is argued that the increased repulsive adsorbate-adsorbate interactions at high coverages must play an important role in determining the adsorption behavior. Therefore, this feature is incorporated through a "coverage-dependent interaction'' model, which introduces a free, adjustable parameter. Another important feature, the site volume reduction, has been treated in two ways: a van der Waal model and a 1D hard-rod theory [van Tassel et al., AIChE J. 40, 925 (1994)]; we have also generalized the latter to include all possible adsorbate overlap scenarios. In particular, the 1D hard-rod model, with our coverage-dependent interaction model, is shown to be in best quantitative agreement with the previous grand canonical Monte Carlo isotherms. The expressions for the isosteric heats of adsorption indicate that attractive and repulsive adsorbate-adsorbate interactions increase and decrease the heats of adsorption, respectively. It is concluded that within the mean field approximation, our simple model for repulsive interactions and the 1D hard-rod model for site volume reduction are able to capture most of the important features of adsorption in confined regions. (C) 1999 American Institute of Physics. [S0021-9606(99)70515-5].

New lithium-ion conductors based on the NASICON structure

Lithium-ion conduction in mixed-metal phosphates, (LiMMIII)-M-V(PO,), [M-V = Nb, Ta; M-III = Al, Cr, Fe], possessing the rhombohedral (R (3) over bar c) NASICON structure has been investigated. Among the phosphates investigated, LiTaAl(PO4)(3) exhibits the highest conductivity, sigma approximate to 1.0 x 10(-2) S cm(-1) at 350 degrees C (E-a = 0.47 eV), comparable to the conductivity of LiTi2(PO4)(3). Unlike LiTi2(PO4)(3) which contains lithium-reducible Ti-IV, LiTaAl(PO4)(3) contains stable Ta-V and Al-III oxidation states and hence deserves further attention towards tailoring new lithium-ion conductors for application as electrolytes in solid state lithium batteries.

Robust controller for an autonomous small refrigeration unit

The authors describe the constructional features of a controller for operating an autonomous refrigeration unit powered by a field of photovoltaic panels and backed up by a generator set. The controller enables three voltage levels of operation of an inverter to meet the start, run and off cycle conditions of the refrigerator compressor. The algorithm considers several input and output parameters and status signals from each subsystem of the unit to deduce a control strategy. Such units find application for storage of vaccines and life-saving medicines requiring uninterrupted refrigeration, in medical shops, rural health centres, veterinary laboratories etc.

Characterization of alkyl chain conformation in an intercalated cationic lipid bilayer by IR spectroscopy

A structural analysis of alkyl chain conformation of an intercalated cationic lipid bilayer is described. Dialkyl dimethylammonium ions (di-C(n)DA) were ion exchanged into the galleries of layered cadmium thiophosphate to give Cd0.83PS3(di-C(n)DA)(0.34). The grafting density and interlayer expansions were identical to those for the intercalated single chain alkyl trimethylammonium (C(n)TA) bilayers. The increased methylene chain density in the galleries, however, forces the intercalated lipid to adopt a more trans ordered structure. Progression bands arising from the coupling of vibrational modes of trans methylene units are used to establish the extent of trans registry. Two types of ordered structures of the intercalated cationic lipid may be distinguished. One in which both alkyl chains adopt an all-trans geometry, and one in which the methylene bond adjacent to the headgroup on one of the alkyl chains is gauche. The latter structure is typically found in the crystalline state of these cationic lipids. The concentrations of the two structures were determined from the ratio of the intensities of the progression bands and were found to remain unchanged with temperature.