Mössbauer Lineshape in the Presence of Radio-Frequency Fields

A general expression for the Mössbauer lineshape in the presence of a radio frequency field is derived. As an example the effect of the rf field on Fe57 nuclei is discussed for a situation where the 3/2 sublevel of 14.4 keV state of Fe57 is selectively populated. At resonance, both the diagonal and non-diagonal matrix elements contribute to the correlation function. As a result, in addition to a slight rf induced distortion of the main Mössbauer line. additional transition lines are obtained. Thus the present calculation supports the experimental observations of Heiman et al.

Stabilization of the collagen structure by hydroxyproline residues

The molecular structure of collagen is now accepted to be based on a triple-stranded coiled-coil, in which the three strands are held together predominantly by hydrogen bonds. Recent experimental evidence has shown that the presence of hydroxyproline residues in the third position of the repeating tripeptide unit lends additional stability to the collagen structure. In this paper, we report a model structure, which is supported by these observations. In a model structure proposed earlier, there are two hydrogen bonds per tripeptide unit, one of which is a direct interchain hydrogen bond, while the second hydrogen bond can be formedvia a water molecule. It has now been shown that the same water molecule can also form a hydrogen bond with the oxygen of theγ-hydroxyl group of hydroxyproline in the third position in the sequence (Gly-R2-R3). This hydroxyl group can also take part in an inter-triple-helix hydrogen bond. Our studies thus show the role played by hydroxyproline residues in the structure and stability of collagen.

Större frihet - bättre lokalt anpassad service? : Förvaltningsreformer och kommunernas service för utvecklingsstörda 1994-2000

In the beginning of the 1990s the legislation regarding the municipalities and the system of central government transfers were reformed in Finland. This resulted in a move from detailed governmental control to increased municipal autonomy. The purpose of this decentralization was to enable the municipalities to better adapt their administration and service supply to local needs. The aim of this study was to explore the effects of the increased municipal autonomy on the organization of services for people with intellectual disabilities. Did the increased autonomy cause the municipalities to alter their service supply and production and did the services become more adapted to local needs? The data consists of statistical information on service use and production, and also of background data such as demographics, economics and political elections on 452 municipalities in Finland from the years 1994 and 2000. The methods used are cluster analysis, discriminant analysis and factor analysis. The municipalities could be grouped in two categories: those which offered mainly one kind of residential services and others which had more varied mixes of services. The use of institutional care had decreased and municipalities which used institutional care as their primary form of service were mostly very small municipalities in 2000. The situation had changed from 1994, when institutional care was the primary service for municipalities of all sizes. Also the service production had become more differentiated and the municipalities had started using more varied ways of production. More municipalities had started producing their own services and private production had increased as well. Furthermore, the increase in local autonomy had opened up possibilities for local politics to influence both the service selection and methods of production. The most significant motive for changes in the service structure was high unemployment and an increasing share of elderly people in the population, particularly in sparsely populated areas. Municipalities with a low level of resources had made more changes in their service organization while those with more resources had been able to carry on as before. Key words: service structure, service for people with intellectual disabilities, municipalities, contingency theory, New Public Management

Mossbauer lineshape in the presence of NMR transitions

The general expression for the Mössbauer lineshape in the presence of radio frequency perturbation derived earlier has been further extended. This involves the calculation of the off-diagonal matrix elements of the correlation function. The results show that there are additional transition lines owing to the nuclear magnetic resonance induced transition in the resonance region. These lines do not show any broadening or splitting. As an example the effect of the rf field on 57Fe nuclei is discussed.

The Linker Region in Receptor Guanylyl Cyclases Is a Key Regulatory Module MUTATIONAL ANALYSIS OF GUANYLYL CYCLASE C

Receptor guanylyl cyclases are multidomain proteins, and ligand binding to the extracellular domain increases the levels of intracellular cGMP. The intracellular domain of these receptors is composed of a kinase homology domain (KHD), a linker of similar to 70 amino acids, followed by the C-terminal guanylyl cyclase domain. Mechanisms by which these receptors are allosterically regulated by ligand binding to the extracellular domain and ATP binding to the KHD are not completely understood. Here we examine the role of the linker region in receptor guanylyl cyclases by a series of point mutations in receptor guanylyl cyclase C. The linker region is predicted to adopt a coiled coil structure and aid in dimerization, but we find that the effects of mutations neither follow a pattern predicted for a coiled coil peptide nor abrogate dimerization. Importantly, this region is critical for repressing the guanylyl cyclase activity of the receptor in the absence of ligand and permitting ligand-mediated activation of the cyclase domain. Mutant receptors with high basal guanylyl cyclase activity show no further activation in the presence of non-ionic detergents, suggesting that hydrophobic interactions in the basal and inactive conformation of the guanylyl cyclase domain are disrupted by mutation. Equivalent mutations in the linker region of guanylyl cyclase A also elevated the basal activity and abolished ligand-and detergent-mediated activation. We, therefore, have defined a key regulatory role for the linker region of receptor guanylyl cyclases which serves as a transducer of information from the extracellular domain via the KHD to the catalytic domain.

Structural and Functional Studies on Trimeric Autotransporters

Trimeric autotransporters are a family of secreted outer membrane proteins in Gram-negative bacteria. These obligate homotrimeric proteins share a conserved C-terminal region, termed the translocation unit. This domain consists of an integral membrane β-barrel anchor and associated α-helices which pass through the pore of the barrel. The α-helices link to the extracellular portion of the protein, the passenger domain. Autotransportation refers to the way in which the passenger domain is secreted into the extracellular space. It appears that the translocation unit mediates the transport of the passenger domain across the outer membrane, and no external factors, such as ATP, ion gradients nor other proteins, are required. The passenger domain of autotransporters contains the specific activities of each protein. These are usually related to virulence. In trimeric autotransporters, the main function of the proteins is to act as adhesins. One such protein is the Yersinia adhesin YadA, found in enteropathogenic species of Yersinia. The main activity of YadA from Y. enterocolitica is to bind collagen, and it also mediates adhesion to other molecules of the extracellular matrix. In addition, YadA is involved in serum resistance, phagocytosis resistance, binding to epithelial cells and autoagglutination. YadA is an essential virulence factor of Y. enterocolitica, and removal of this protein from the bacteria leads to avirulence. In this study, I investigated the YadA-collagen interaction by studying the binding of YadA to collagen-mimicking peptides by several biochemical and biophysical methods. YadA bound as tightly to the triple-helical model peptide (Pro-Hyp-Gly)10 as to native collagen type I. However, YadA failed to bind a similar peptide that does not form a collagenous triple helix. As (Pro-Hyp-Gly)10 does not contain a specific sequence, we concluded that a triple-helical conformation is necessary for YadA binding, but no specific sequence is required. To further investigate binding determinants for YadA in collagens, I examined the binding of YadA to a library of collagen-mimicking peptides that span the entire triple-helical sequences of human collagens type II and type III. YadA bound promiscuously to many but not all peptides, indicating that a triple-helical conformation alone is not sufficient for binding. The high-binding peptides did not share a clear binding motif, but these peptides were rich in hydroxyproline residues and contained a low number of charged residues. YadA thus binds collagens without sequence specificity. This strategy of promiscuous binding may be advantageous for pathogenic bacteria. The Eib proteins from Escherichia coli are immunoglobulin (Ig)-binding homologues of YadA. I showed conclusively that recombinant EibA, EibC, EibD and EibF bind to IgG Fc. I crystallised a fragment of the passenger domain of EibD, which binds IgA in addition to IgG. The structure has a YadA-like head domain and an extended coiled-coil stalk. The top half of the coiled-coil is right-handed with hendecad periodicity, whereas the lower half is a canonical left-handed coiled-coil. At the transition from right- to left-handedness, a small β-sheet protrudes from each monomer. I was able to map the binding regions for IgG and IgA using truncations and site-directed mutagenesis to the coiled-coil stalk and identified residues critical for Ig binding.

Lidar heat map based channel sounding for complex wireless environments

This thesis is a development of a methodology to predict the radio transmitter signal attenuation, via vertical density profiling of digitised objects, through the use of Light Detection and Ranging (LiDaR) measurements. The resulting map of indexed signal attenuation is useful for dynamic radio transmitter placement within the geospatial data set without expensive and tedious radio measurements.

The role of cyclase-associated protein (CAP) in actin dynamics during cell motility and morphogenesis

The highly dynamic remodeling of the actin cytoskeleton is responsible for most motile and morphogenetic processes in all eukaryotic cells. In order to generate appropriate spatial and temporal movements, the actin dynamics must be under tight control of an array of actin binding proteins (ABPs). Many proteins have been shown to play a specific role in actin filament growth or disassembly of older filaments. Very little is known about the proteins affecting recycling i.e. the step where newly depolymerized actin monomers are funneled into new rounds of filament assembly. A central protein family involved in the regulation of actin turnover is cyclase-associated proteins (CAP, called Srv2 in budding yeast). This 50-60 kDa protein was first identified from yeast as a suppressor of an activated RAS-allele and a factor associated with adenylyl cyclase. The CAP proteins harbor N-terminal coiled-coil (cc) domain, originally identified as a site for adenylyl cyclase binding. In the N-terminal half is also a 14-3-3 like domain, which is followed by central proline-rich domains and the WH2 domain. In the C-terminal end locates the highly conserved ADP-G-actin binding domain. In this study, we identified two previously suggested but poorly characterized interaction partners for Srv2/CAP: profilin and ADF/cofilin. Profilins are small proteins (12-16 kDa) that bind ATP-actin monomers and promote the nucleotide exchange of actin. The profilin-ATP-actin complex can be directly targeted to the growth of the filament barbed ends capped by Ena/VASP or formins. ADF/cofilins are also small (13-19 kDa) and highly conserved actin binding proteins. They depolymerize ADP-actin monomers from filament pointed ends and remain bound to ADP-actin strongly inhibiting nucleotide exchange. We revealed that the ADP-actin-cofilin complex is able to directly interact with the 14-3-3 like domain at the N-terminal region of Srv2/CAP. The C-terminal high affinity ADP-actin binding site of Srv2/CAP competes with cofilin for an actin monomer. Cofilin can thus be released from Srv2/CAP for the subsequent round of depolymerization. We also revealed that profilin interacts with the first proline-rich region of Srv2/CAP and that the binding occurs simultaneously with ADP-actin binding to C-terminal domain of Srv2/CAP. Both profilin and Srv2/CAP can promote nucleotide exchange of actin monomer. Because profilin has much higher affinity to ATP-actin than Srv2/CAP, the ATP-actin-profilin complex is released for filament polymerization. While a disruption of cofilin binding in yeast Srv2/CAP produces a severe phenotype comparable to Srv2/CAP deletion, an impairment of profilin binding from Srv2/CAP results in much milder phenotype. This suggests that the interaction with cofilin is essential for the function of Srv2/CAP, whereas profilin can also promote its function without direct interaction with Srv2/CAP. We also show that two CAP isoforms with specific expression patterns are present in mice. CAP1 is the major isoform in most tissues, while CAP2 is predominantly expressed in muscles. Deletion of CAP1 from non-muscle cells results in severe actin phenotype accompanied with mislocalization of cofilin to cytoplasmic aggregates. Together these studies suggest that Srv2/CAP recycles actin monomers from cofilin to profilin and thus it plays a central role in actin dynamics in both yeast and mammalian cells.

Free energy calculations of the interactions of c-Jun-based synthetic peptides with the c-Fos protein

The c-Fos–c-Jun complex forms the activator protein 1 transcription factor, a therapeutic target in the treatment of cancer. Various synthetic peptides have been designed to try to selectively disrupt the interaction between c-Fos and c-Jun at its leucine zipper domain. To evaluate the binding affinity between these synthetic peptides and c-Fos, polarizable and nonpolarizable molecular dynamics (MD) simulations were conducted, and the resulting conformations were analyzed using the molecular mechanics generalized Born surface area (MM/GBSA) method to compute free energies of binding. In contrast to empirical and semiempirical approaches, the estimation of free energies of binding using a combination of MD simulations and the MM/GBSA approach takes into account dynamical properties such as conformational changes, as well as solvation effects and hydrophobic and hydrophilic interactions. The predicted binding affinities of the series of c-Jun-based peptides targeting the c-Fos peptide show good correlation with experimental melting temperatures. This provides the basis for the rational design of peptides based on internal, van der Waals, and electrostatic interactions.

Transcriptional activation of the Escherichia coli bgl operon: negative regulation by DNA structural elements near the promoter

The bgl operon of Escherichia coil is transcriptionally inactive in wild-type cells. DNA insertion sequences (IS) constitute a major class of spontaneous mutations that activate the cryptic bgl promoter. In an attempt to study the molecular mechanism of activation mediated by insertion sequences, transcription of the bgl promoter was carried out in vitro. Stimulation of transcription is observed when a plasmid containing an insertionally activated bgl promoter is used as a template in the absence of proteins other than RNA polymerase. Deletions that remove sequences upstream of the bgl promoter, and insertion of a 1.2 kb DNA fragment encoding resistance to kanamycin, activate the promoter. Point mutations within a region of dyad symmetry upstream of the promoter, which has the potential to extrude into a cruciform structure under torsional stress, also lead to activation, Introduction of a sequence with dyad symmetry, upstream of an activated bgl promoter carrying a deletion of upstream sequences, results in a fourfold reduction in transcription, These results suggest that the cryptic nature of the bgl promoter is because of the presence of DNA structural elements near the promoter that negatively affect transcription.

Integrated CMOS Gas Sensors

We present a low power gas sensor system on CMOS platform consisting of micromachined polysilicon microheater, temperature controller circuit, resistance readout circuit and SnO2 transducer film. The design criteria for different building blocks of the system is elaborated The microheaters are optimized for temperature uniformity as well as static and dynamic response. The electrical equivalent model for the microheater is derived by extracting thermal and mechanical poles through extensive laser doppler vibrometer measurements. The temperature controller and readout circuit are realized on 130nm CMOS technology The temperature controller re-uses the heater as a temperature sensor and controls the duty cycle of the waveform driving the gate of the power MOSFET which supplies heater current. The readout circuit, with subthreshold operation of the MOSFETs, is based oil resistance to time period conversion followed by frequency to digital converter Subthreshold operatin of MOSFETs coupled with sub-ranging technique, achieves ultra low power consumption with more than five orders of magnitude dynamic range RF sputtered SnO2 film is optimized for its microstructure to achive high sensitivity to sense LPG gas.

Off-axis field approximations for ion traps with apertures

In recent work (Int. J. Mass Spec., vol. 282, pp. 112–122) we have considered the effect of apertures on the fields inside rf traps at points on the trap axis. We now complement and complete that work by considering off-axis fields in axially symmetric (referred to as “3D”) and in two dimensional (“2D”) ion traps whose electrodes have apertures, i.e., holes in 3D and slits in 2D. Our approximation has two parts. The first, EnoAperture, is the field obtained numerically for the trap under study with apertures artificially closed. We have used the boundary element method (BEM) for obtaining this field. The second part, EdueToAperture, is an analytical expression for the field contribution of the aperture. In EdueToAperture, aperture size is a free parameter. A key element in our approximation is the electrostatic field near an infinite thin plate with an aperture, and with different constant-valued far field intensities on either side. Compact expressions for this field can be found using separation of variables, wherein the choice of coordinate system is crucial. This field is, in turn, used four times within our trap-specific approximation. The off-axis field expressions for the 3D geometries were tested on the quadrupole ion trap (QIT) and the cylindrical ion trap (CIT), and the corresponding expressions for the 2D geometries were tested on the linear ion trap (LIT) and the rectilinear ion trap (RIT). For each geometry, we have considered apertures which are 10%, 30%, and 50% of the trap dimension. We have found that our analytical correction term EdueToAperture, though based on a classical small-aperture approximation, gives good results even for relatively large apertures.

Switchable-feed reconfigurable ultra-wide band planar antenna

Reconfigurable antennas capable of radiating in only specific desired directions increase system functionality in applications like direction finding and beam steering. This paper presents the design simulation, fabrication and measurement of a horizontally polarized, direction reconfigurable Vivaldi antenna, designed for the lower-band UWB (2-6 GHz). This design employs eight circularly distributed independent Vivaldi antennas with a common port, electronically controlled by PIN diodes acting as RF switches. Experimental results show that the reconfigurable antenna has a bandwidth of 4 GHz (2-6 GHz), with 5 dB gain in the desired direction and capable of steering over the 360° range.

Electronically-reconfigurable horizontally polarized wide-band planar antenna

Antennas are a necessary and critical component of communications and radar systems, but their inability to adjust to new operating scenarios can sometimes limit the system performance. Reconfigurable antennas capable of radiating in only specific desired directions can ameliorate these restrictions and help to achieve increased functionality in applications like direction finding and beam steering. This paper presents the design simulation, fabrication and measurement of a wide-band, horizontally polarized, direction reconfigurable microstrip antenna operating at 2.45 GHz. The design employs a central horizontally polarized omnidirectional active element surrounded by electronically reconfigurable parasitic microstrip elements, controlled by PIN diodes acting as RF switches. Experimental results show that the reconfigurable antenna has a bandwidth of 40% (2-3 GHz), with 3 dB gain in the desired direction and capable of steering over the 360° range.

Multiple conformational states in crystals and in solution in alpha gamma hybrid peptides. Fragility of the C-12 helix in short sequences

The conformational properties of foldamers generated from alpha gamma hybrid peptide sequences have been probed in the model sequence Boc-Aib-Gpn-Aib-Gpn-NHMe. The choice of alpha-aminoisobutyryl (Aib) and gabapentin (Gpn) residues greatly restricts sterically accessible coil formational space. This model sequence was anticipated to be a short segment of the alpha gamma C-12 helix, stabilized by three successive 4 -> 1 hydrogen bonds, corresponding to a backbone-expanded analogue of the alpha polypeptide 3(10)-helix. Unexpectedly, three distinct crystalline polymorphs were characterized in the solid state by X-ray diffraction. In one form, two successive C-12 hydrogen bonds were obtained at the N-terminus, while a novel C-17 hydrogen-bonded gamma alpha gamma turn was observed at the C-terminus. In the other two polymorphs, isolated C-9 and C-7 hydrogen-bonded turns were observed at Gpn (2) and Gpn (4). Isolated C-12 and C-9 turns were also crystallographically established in the peptides Boc-Aib-Gpn-Aib-OMe and Boc-Gpn-Aib-NHMe, respectively. Selective line broadening of NH resonances and the observation of medium range NH(i)<-> NH(i+2) NOEs established the presence of conformational heterogeneity for the tetrapeptide in CDCl3 solution. The NMR results are consistent with the limited population of the continuous C-12 helix conformation. Lengthening of the (alpha gamma)(n) sequences in the nonapeptides Boc-Aib-Gpn-Aib-Gpn-Aib-Gpn-Aib-Gpn-Xxx (Xxx = Aib, Leu) resulted in the observation of all of the sequential NOEs characteristic of an alpha gamma C-12 helix. These results establish that conformational fragility is manifested in short hybrid alpha gamma sequences despite the choice of conformationally constrained residues, while stable helices are formed on chain extension.