An induction gene trap screen in embryonic stem cells: Identification of genes that respond to retinoic acid in vitro.

We have developed a novel induction gene trap approach that preselects in vitro for integrations into genes that lie downstream of receptor/ligand-mediated signaling pathways. Using this approach, we have identified 20 gene trap integrations in embryonic stem cells, 9 of which were induced and 11 of which were repressed after exposure to exogenous retinoic acid (RA). All but one of these integrations showed unique spatially restricted or tissue-specific patterns of expression between 8.5 and 11.5 days of embryogenesis. Interestingly, expression was observed in tissues that are affected by alterations in RA levels during embryogenesis. Sequence analysis of fusion transcripts from six integrations revealed five novel gene sequences and the previously identified protooncogene c-fyn. To date, germ-line transmission and breeding has uncovered one homozygous embryonic lethal and three homozygous viable insertions. These studies demonstrate the potential of this induction gene trap approach for identifying and mutating genes downstream of signal transduction pathways.

Molecular organization of histidine-tagged biomolecules at self-assembled lipid interfaces using a novel class of chelator lipids.

In molecular biology, the expression of fusion proteins is a very useful and well-established technique for the identification and one-step purification of gene products. Even a short fused sequence of five or six histidines enables proteins to bind to an immobilized metal ion chelate complex. By synthesis of a class of chelator lipids, we have transferred this approach to the concept of self-assembly. The specific interaction and lateral organization of a fluorescent fusion molecule containing a C-terminal oligohistidine sequence was studied by film balance techniques in combination with epifluorescence microscopy. Due to the phase behavior of the various lipid mixtures used, the chelator lipids can be laterally structured, generating two-dimensional arrays of histidine-tagged biomolecules. Because of the large variety of fusion proteins already available, this concept represents a powerful technique for orientation and organization of proteins at lipid interfaces with applications in biosensing, biofunctionalization of nanostructured interfaces, two-dimensional crystallization, and studies of lipid-anchored proteins.

On the pragmatics of social theory. The case of Elias's "On the Process of Civilization"

This paper proposes a new approach to the study of sociological classics. This approach is pragmatic in character. It draws upon the social pragmatism of G.H. Mead and the sociology of texts of D.F. McKenzie. Our object of study is Norbert Elias’s On the Process of Civilization. The pragmatic genealogy of this book reveals the importance of taking materiality seriously. By documenting the successive entanglements between human agency and non-human factors, we discuss the origins of the book in the 1930s, how it was forgotten for thirty years, and how in the mid-1970s it became a sociological classic. We explain canonization as a matter of fusion between book’s material form and its content, in the context of the paperback revolution of the 1960s, the events of May 1968, and the demise of Parsons’ structural functionalism, and how this provided Elias with an opportunity to advance his model of sociology.

Non-Viral Gene Therapy to Cells of the bovine Intervertebral Disc

Background. Low back pain is an increasing global health problem, which is associated with intervertebral disc (IVD) damage and degeneration. Major changes occur in the nucleus pulposus (NP), with the degradation of the extracellular matrix (ECM).1 Further studies showed that growth factors from transforming growth factor β (TGFβ) and bone morphogenic proteins (BMP) family may induce chondrogenic differentiation of mesenchymal stem cells (MSC).2 Focusing on non-viral gene therapies and their possible translation into the clinics, we investigated if GDF6 (syn. BMP13 or CDMP2) can induce regeneration of degraded NP. We hypothesized that IVD transfected with plasmid over-expressing GDF6 also up-regulates other NP- and chondrogenic cell markers and enhances ECM deposition. Methods. Bovine nucleus pulposus (bNPC) and annulus fibrosus cells (bAFC) were harvested from bovine coccygeal IVD. Primary cells were then electroporized with plasmid GDF6 (Origene, vector RG211366) by optimizing parameters using the Neon Transfection system (Life Technologies, Basel). After transfection, cells were cultured in 2D monolayer or 3D alginate beads for 7, 14 or 21 days. Transfection efficiency of pGDF6 was analyzed by immunohistochemistry and fluorescent microscopy. Cell phenotype was quantified by real-time RT-PCR. To test a non-viral gene therapy applied directly to 3D whole organ culture, coccygeal bovine IVDs were harvested as previously described. Bovine IVDs were transfected by injection of plasmid GDF6 into the center. Electroporation was performed with ECM830 Square Wave Electroporation System (Harvard Apparatus, MA) using 2-needle array electrode or tweezertrodes. 72 h after tranfection discs were fixed and cryosectioned and analyzed by immunofluorescence against GDF6. Results. RT-PCR and immunohistochemistry confirmed up-regulation of GFP and GDF6 in the primary bNPC/bAFC culture. The GFP-tagged GDF6 protein, however, was not visible, possibly due to failure of dimer formation as a result of fusion structure. Organ IVD culture transfection revealed GDF6 positive staining in the center of the disc using 2-needle array electrode. Results from tweezertrodes did not show any GDF6 positive cells. Conclusion. Non-viral transfection is an appealing approach for gene therapy as it fulfills the translational safety aspects of transiency and lacks the toxic effects of viral transduction. We identified novel parameters to successfully transfect primary bovine IVD cells. For transfection of whole IVD explants electroporation parameters need to be further optimized. Acknowledgements. This project was funded by the Lindenhof Foundation (Funds “Research & Teaching”) Project no. 13-02-F. The imaging part of this study was performed with the facility of the Microscopy Imaging Center (MIC), University of Bern. References. Roughly PJ (2004): Spine (Phila), 29:2691-2699 Clarke LE, McConell JC, Sherratt MJ, Derby B, Richardson SM, Hoyland JA (2014), Arthritis Research & Therapy, 16:R67

The Contribution of the Activation Entropy to the Gas-Phase Stability of Modified Nucleic Acid Duplexes

Tricyclo-DNA (tcDNA) is a sugar-modified analogue of DNA currently tested for the treatment of Duchenne muscular dystrophy in an antisense approach. Tandem mass spectrometry plays a key role in modern medical diagnostics and has become a widespread technique for the structure elucidation and quantification of antisense oligonucleotides. Herein, mechanistic aspects of the fragmentation of tcDNA are discussed, which lay the basis for reliable sequencing and quantification of the antisense oligonucleotide. Excellent selectivity of tcDNA for complementary RNA is demonstrated in direct competition experiments. Moreover, the kinetic stability and fragmentation pattern of matched and mismatched tcDNA heteroduplexes were investigated and compared with non-modified DNA and RNA duplexes. Although the separation of the constituting strands is the entropy-favored fragmentation pathway of all nucleic acid duplexes, it was found to be only a minor pathway of tcDNA duplexes. The modified hybrid duplexes preferentially undergo neutral base loss and backbone cleavage. This difference is due to the low activation entropy for the strand dissociation of modified duplexes that arises from the conformational constraint of the tc-sugar-moiety. The low activation entropy results in a relatively high free activation enthalpy for the dissociation comparable to the free activation enthalpy of the alternative reaction pathway, the release of a nucleobase. The gas-phase behavior of tcDNA duplexes illustrates the impact of the activation entropy on the fragmentation kinetics and suggests that tandem mass spectrometric experiments are not suited to determine the relative stability of different types of nucleic acid duplexes.

Structural Insights into Viral Membrane Fusion Machinery via Cryo-Electron Tomography: Influenza Virus and Human Parainfluenza Virus

Thesis (Ph.D.)--University of Washington, 2016-06

The plasticisation effect of glycerol and water on the gelatinisation of wheat starch

In the extrusion manufacture of starch-based thermoplastics, such as biodegradable packaging materials, glycerol is an effective additive as a plasticiser, that is, to diminish the brittle nature of the product and provide the desired extent of flexibility. However, the addition of glycerol may also affect the gelatinisation behaviour of the starch-water mixture, and hence the required processing conditions for producing a homogeneously gelatinised starch-based material. The effect of glycerol on the gelatinisation of wheat starch was studied using differential scanning calorimetry (DSC). Mixtures of starch, water and glycerol were investigated with a water content ranging from 12 - 40% and a glycerol concentration up to 75%. Dependent on composition, the enthalpy of gelatinisation ranged from 1.7 - 12.6 J/g (on a dry starch basis), while the onset and peak temperatures varied from 54 to 86 degreesC and 60 to 90 degreesC, respectively. As expected, water acted as a plasticiser in that the onset temperature for gelatinisation (TO) decreased with increasing moisture content. Glycerol, however, increased To. It is shown that the T-0 of starch-glycerol-water mixtures may be predicted on the basis of the effective moisture content of the starch fraction of these mixtures resulting from the relative speed of moisture absorption by glycerol and starch, respectively. Moisture sorption kinetics of wheat starch and glycerol in 100% relative humidity were determined and used to predict the preferential water absorption by glycerol in starch-glycerol-water mixtures and hence the resulting T-0 of the system.

Gelatinisation of starch in mixtures of sugars. II. Application of differential scanning calorimetry

Differential scanning calorimetry was used to investigate the effect of mixtures of glucose and fructose, and five types of honeys on starch gelatinisation. At a 1:1 starch:water ratio, glucose generally increased the enthalpy (DeltaH(gel)) and temperatures (T-onset, T-peak and T-end) of gelatinisation more than fructose. Upon mixing, DeltaH(gel) of the low-temperature endotherm decreased in comparison to the sole sugars, but was fairly constant (7.7 +/- 0.33 J/g dry starch). DeltaH(gel) of the high-temperature endotherm increased with the fructose content. For both endotherms, the gelatinisation temperatures were unchanged (CV less than or equal to 3%) for the mixtures. With the honeys (moisture, 14.9-18.0%; fructose, 37.2-44.0%; glucose, 28.3-31.9%) added at 1.1-4.4 g per g dry starch, the enthalpy and temperatures of gelatinisation did not vary significantly (CV less than or equal to 6%). Typical thermograms are presented, and the results are interpreted in the light of the various proposed mechanisms for starch gelatinisation in sugar-water systems, total sugar content and possible sugar-sugar interactions. The thermograms were broader in the presence of the sugars and honeys, and a biphasic character was consistently exhibited. The application of an exponential equation to the gelatinisation temperatures of the starch-honey mixtures revealed an opposing influence of fructose and glucose during gelatinisation. The mechanism of starch gelatinisation may be better understood if techniques could be perfected to quantify breakage and formation of hydrogen bonds in the starch granules, and suggested techniques are discussed. (C) 2004 Elsevier Ltd. All rights reserved.

Investigation of the starch gelatinisation phenomena in water-glycerol systems: application of modulated temperature differential scanning calorimetry

The use of modulated temperature differential scanning calorimetry (MTDSC) has provided further insight into the gelatinisation process since it allows the detection of glass transition during gelatinisation process. It was found in this work that the glass transition overlapped with the gelatinisation peak temperature for all maize starch formulations studied. Systematic investigation on maize starch gelatinisation over a range of water-glycerol concentrations with MTDSC revealed that the addition of glycerol increased the gelatinisation onset temperature with an extent that depended on the water content in the system. Furthermore, the addition of glycerol promoted starch gelatinisation at low water content (0.4 g water/g dry starch) and the enthalpy of gelatinisation varied with glycerol concentration (0.73-19.61 J/g dry starch) depending on the water content and starch type. The validities of published gelatinisation models were explored. These models failed to explain the glass transition phenomena observed during the course of gelatinisation and failed to describe the gelatinisation behaviour observed over the water-glycerol concentrations range investigated. A hypothesis for the mechanisms involved during gelatinisation was proposed based on the side chain liquid crystalline polymer model for starch structure and the concept that the order-disorder transition in starch requires that the hydrogen bonds (the major structural element in the granule packing) to be broken before the collapse of order (helix-coil transition) can take place. (C) 2004 Elsevier Ltd. All rights reserved.

Phosphatidylinositol 3-kinase C2 alpha is essential for ATP-dependent priming of neurosecretory granule exocytosis

Neurotransmitter release and hormonal secretion are highly regulated processes culminating in the calcium-dependent fusion of secretory vesicles with the plasma membrane. Here, we have identified a role for phosphatidylinositol 3-kinase C2 alpha (PI3K-C2 alpha) and its main catalytic product, PtdIns3P, in regulated exocytosis. In neuroendocrine cells, PI3K-C2 alpha is present on a subpopulation of mature secretory granules. Impairment of PI3K-C2 alpha function specifically inhibits the ATP-dependent priming phase of exocytosis. Overexpression of wild-type PI3K-C2 alpha enhanced secretion, whereas transfection of PC12 cells with a catalytically inactive PI3K-C2 alpha mutant or a 2xFYVE domain sequestering PtdIns3P abolished secretion. Based on these results, we propose that production of PtdIns3P by PI3K-C2 alpha is required for acquisition of fusion competence in neurosecretion.

Grand canonical Monte Carlo simulation study of methane adsorption at an open graphite surface and in slitlike carbon pores at 273 K

Grand canonical Monte Carlo (GCMC) simulation was used for the systematic investigation of the supercritical methane adsorption at 273 K on an open graphite surface and in slitlike micropores of different sizes. For both considered adsorption systems the calculated excess adsorption isotherms exhibit a maximum. The effect of the pore size on the maximum surface excess and isosteric enthalpy of adsorption for methane storage at 273 K is discussed. The microscopic detailed picture of methane densification near the homogeneous graphite wall and in slitlike pores at 273 K is presented with selected local density profiles and snapshots. Finally, the reliable pore size distributions, obtained in the range of the microporosity, for two pitch-based microporous activated carbon fibers are calculated from the local excess adsorption isotherms obtained via the GCMC simulation. The current systematic study of supercritical methane adsorption both on an open graphite surface and in slitlike micropores performed by the GCMC summarizes recent investigations performed at slightly different temperatures and usually a lower pressure range by advanced methods based on the statistical thermodynamics.

Interpretation of the temperature dependence of rate constants in biosensor studies

A comparison is made between Arrhenius and transition-state analyses of the temperature dependence of rate constants reported in four published biosensor studies. Although the Eyring transition-state theory seemingly affords a more definitive solution to the problem of characterizing the activation energetics, the analysis is equivocal because of inherent assumptions about reaction mechanism and the magnitude of the transmission coefficient. In view of those uncertainties it is suggested that a preferable course of action entails reversion to the empirical Arrhenius analysis with regard to the energy of activation and a preexponential factor. The former is essentially equivalent to the enthalpy of activation, whereas the magnitude of the latter indicates directly the extent of disparity between the frequency of product formation and the universal frequency factor (temperature multiplied by the ratio of the Boltzmann and Planck constants) and hence the likelihood of a more complicated kinetic mechanism than that encompassed by the Eyring transition-state theory. (C) 2004 Elsevier Inc. All rights reserved.

Performance of a scramjet combustor with combined normal and tangential fuel injection

The performance of a scramjet combustor with combined normal and tangential injection was experimentally investigated. Experiments were performed on a 500-mm cylindrical scramjet combustor at a freestream Mach number of 4.5, a nozzle supply pressure of 35.8 MPa, and a nozzle supply enthalpy of 5.8 MJ/kg. Hydrogen fuel was injected normally through portholes to promote combustion and tangentially through a slot to reduce viscous drag. A series of fuel injectors were used to vary the proportion of tangential to normal fuel between 45 and 100%. Reductions in the viscous drag of up to 25% were observed with the greatest reductions occurring at the lowest total equivalence ratio tested for each injector. However, the average pressure produced by combustion with combined normal and tangential injection was approximately 50% less than that produced by normal injection alone. An analysis of the change in specific impulse of the scramjet combustor indicated that the best overall performance was produced by 100% normal injection.

Flow patterns and performance of distillation trays

It is known that distillation tray efficiency depends on the liquid flow pattern, particularly for large diameter trays. Scale·up failures due to liquid channelling have occurred, and it is known that fitting flow control devices to trays sometirr.es improves tray efficiency. Several theoretical models which explain these observations have been published. Further progress in understanding is at present blocked by lack of experimental measurements of the pattern of liquid concentration over the tray. Flow pattern effects are expected to be significant only on commercial size trays of a large diameter and the lack of data is a result of the costs, risks and difficulty of making these measurements on full scale production columns. This work presents a new experiment which simulates distillation by water cooling. and provides a means of testing commercial size trays in the laboratory. Hot water is fed on to the tray and cooled by air forced through the perforations. The analogy between heat and mass transfer shows that the water temperature at any point is analogous to liquid concentration and the enthalpy of the air is analogous to vapour concentration. The effect of the liquid flow pattern on mass transfer is revealed by the temperature field on the tray. The experiment was implemented and evaluated in a column of 1.2 m. dia. The water temperatures were measured by thennocouples interfaced to an electronic computerised data logging system. The "best surface" through the experimental temperature measurements was obtained by the mathematical technique of B. splines, and presented in tenos of lines of constant temperature. The results revealed that in general liquid channelling is more imponant in the bubbly "mixed" regime than in the spray regime. However, it was observed that severe channelling also occurred for intense spray at incipient flood conditions. This is an unexpected result. A computer program was written to calculate point efficiency as well as tray efficiency, and the results were compared with distillation efficiencies for similar loadings. The theoretical model of Porter and Lockett for predicting distillation was modified to predict water cooling and the theoretical predictions were shown to be similar to the experimental temperature profiles. A comparison of the repeatability of the experiments with an errors analysis revealed that accurate tray efficiency measurements require temperature measurements to better than ± 0.1 °c which is achievable with conventional techniques. This was not achieved in this work, and resulted in considerable scatter in the efficiency results. Nevertheless it is concluded that the new experiment is a valuable tool for investigating the effect of the liquid flow pattern on tray mass transfer.

A study of the scattering of fast neutrons in large samples

In the present work, the elastic scattering of fast neutrons from iron and concrete samples were studied at incident neutron energies of 14.0 and 14.4 Mev, using a neutron spectrometer based on the associated particle time-of-flight technique. These samples were chosen because of their importance in the design of fusion reactor shielding and construction. Using the S.A.M.E.S. accelerator and the 3 M v Dynamitron accelerator at the Radiation Centre, 14.0 and 14.4 Mev neutrons were produced by the T(d, n)4He reaction at incident deuteron energies of 140 keV and 900 keV mass III ions respectively. The time of origin of the neutron was determined by detecting the associated alpha particles. The samples used were extended flat plates of thicknesses up to 1.73 mean free paths for iron and 2.3 mean free paths for concrete. The associated alpha particles and fast neutrons were detected by means of a plastic scintillator mounted on a fast focused photomultiplier tube. The differential neutron elastic scattering cross-sections were measured for 14 Mev neutrons in various thicknesses of iron and concrete in the angular range from zero to 90°. In addition, the angular distributions of 14.4 Mev neutrons after passing through extended samples of iron were measured at several scattering angles in the same angular range. The measurements obtained for the thin sample of iron were compared with the results of Coon et al. The differential cross-sections for the thin iron sample were also analyzed on the optical model using the computer code RAROMP. For the concrete sample, the angular distribution of the thin sample was compared with the cross-sections calculated from the major constituent elements of concrete, and with the predicted values of the optical model for those elements. No published data could be found to compare with the results of the concrete differential cross-sections. In the case of thick samples of iron and concrete, the number of scattered neutrons were compared with a phenomological calculation based on the continuous slowing down model. The variation of measured cross-sections with sample thickness were found to follow the empirical relation σ = σ0 eαx. By using the universal constant "K", good fits were obtained to the experimental data. In parallel with the work at 14.0 and 14.4 Mev, an associated particle time-of-flight spectrometer was investigated which used the 2H(d,n)3He reaction for 3.02 Mev neutron energy at the incident deuteron energy of 1 Mev.