Cage Configuration Research Articles

Amplified electrochemical DNA sensor using peroxidase-like DNAzyme

A novel electrochemical DNA sensor was developed here by using peroxidase-like G-quadruplex-based DNAzyme as a biocatalytic label. A hairpin structure including the G-quadruplex-based DNAzyme in a caged configuration and the target DNA probe were immobilized on Au-electrode surface. Upon hybridization with the target, the hairpin structure was opened, and the G-quadruplex-based DNAzyme was generated on the electrode surface, triggering the electrochemical oxidization of hydroquinone by H 2O 2, which provide a quantitative measure for the detection of the target DNA. The DNA target was analyzed with a detection limit of 0.6 nM. This method is simple and easy to design without direct conjugation of redox-active element.

Modeling and identification of an electro-mechanical system: The LISA grabbing positioning and release mechanism case

In the frame of space missions, mechanisms often constitute critical systems whose functionality and performance need to be tested on ground before the mission launch. The LISA scientific space mission will detect gravitational waves by measuring the relative displacement of pairs of free-floating test masses set into geodesic motion onboard of three spacecrafts. Inside each satellite, the injection of the test masses from the caged configuration into the geodesic trajectory will be performed by the grabbing positioning and release mechanism. To provide a successful injection, the test masses must be dynamically released with a minimal residual velocity against adhesion with the holding device. A parameter that determines the test mass residual velocity is the quickness of the retraction of the holding device. The need arises then to characterize the dynamic response of the release mechanism in order to predict its behaviour in the in-flight conditions. Once a validated model of the mechanism is available, the compliance of the system to the tight requirement on the maximum allowed residual velocity of the test mass may be verified. Starting from an electro-mechanical model of the mechanism dynamics, this paper presents the results of the experimental identification of its relevant parameters.

Amplified Biosensing Using the Horseradish Peroxidase-Mimicking DNAzyme as an Electrocatalyst

The hemin/G-quadruplex horseradish peroxidase-mimicking DNAzyme is assembled on Au electrodes. It reveals bioelectrocatalytic properties and electrocatalyzes the reduction of H(2)O(2). The bioelectrocatalytic functions of the hemin/G-quadruplex DNAzyme are used to develop electrochemical sensors that follow the activity of glucose oxidase and biosensors for the detection of DNA or low-molecular-weight substrates (adenosine monophosphate, AMP). Hairpin nucleic structures that include the G-quadruplex sequence in a caged configuration and the nucleic acid sequence complementary to the analyte DNA, or the aptamer sequence for AMP, are immobilized on Au-electrode surfaces. In the presence of the DNA analyte, or AMP, the hairpin structures are opened, and the hemin/G-quadruplex horseradish peroxidase-mimicking DNAzyme structures are generated on the electrode surfaces. The bioelectrocatalytic cathodic currents generated by the functionalized electrodes, upon the electrochemical reduction of H(2)O(2), provide a quantitative measure for the detection of the target analytes. The DNA target was analyzed with a detection limit of 1 x 10(-12) M, while the detection limit for analyzing AMP was 1 x 10(-6) M. Methods to regenerate the sensing surfaces are presented.

Functionalized Carborane Complexes of the [M(CO)2(NO)]2+ Core (M = 99mTc, Re): A New Class of Organometallic Probes for Correlated in Vitro and in Vivo Imaging

Functionalized carborane complexes of the [M(CO)2(NO)]2+ (M = Re, 99mTc) core have potential utility as matched pairs of probes for correlated optical (M = Re) and scintigraphic (M = 99mTc) imaging. A synthetic route to closo-rhenacarboranes of the type [Re(CO)2(NO)(RR′C2B9H9)] in a manner suitable for the preparation of the radioactive technetium-99m analogues has been developed, resulting in the isolation of four novel metallacarboranes [Re(CO)2(NO)(RR′C2B9H9)], which exhibit both 3,1,2 (6a: R = H, R′ = Bn) and 2,1,8 (7a: R = R′ = H; 8a: R = H, R′ = Ph; 9a: R = R′ = Bn) cage configurations. These complexes absorb strongly at 300−348 nm; 6a−9a fluoresce weakly at ambient temperature following excitation at 300 nm (7a) or ∼340 nm (6a, 8a/9a), with emission maxima ranging between 313 and 411 nm. A microwave-assisted approach was used to prepare radioactive [99mTc(CO)3]+-carborane complexes (1b−4b) at the tracer level. When an analogous aqueous nitrosation methodology was applied to generate dicarbonylnitroso-closo-technetacarboranes, the novel complexes 6b, 8b, and 9b were isolated in good radiochemical yields (62−79%). In aqueous solutions, slow decomposition of 6b and 8b, but not 9b was observed. To better understand this process, the radioactive 186/188Re analogue of 8a was also prepared.

Experimental correlation of nitroxide recollision spin exchange with free volume and compressibility in alkane and aromatic compounds

Diffusion of perdeuterated tempone (PDT) in various nonpolar hydrocarbon solvents on both the large and microscopic scales is examined through electron paramagnetic resonance spectroscopy. Spectral line broadening and hyperfine spacing are measured in order to extract both the Heisenberg spin-exchange rate as well as the average recollision times between spin-probe pairs. Probe recollision is responsible for a linear component to the dependence of the line shift on spectral broadening which has been identified in recent years. The present study extends the work of a previous paper by Kurban et al. [J. Chem. Phys. 129, 064501 (2008)], in which it was reported that recollision rates for PDT formed a common curve across n-alkanes when plotted with respect to free volume and to isothermal compressibility. It is now found that such common curves occur within distinct chemical families, in particular, the alkane and aromatic groups. Within each chemical family, the spin probe recollision rate correlates with free volume and compressibility independently of the geometry of the particular solvent. All solvents show significantly enhanced recollisional diffusion over the Stokes-Einstein (SE) prediction at high temperatures. The spin-exchange rate forms a common curve with respect to T/eta for all alkanes except cyclohexane and another common curve in all three aromatic compounds. It is reasoned that although all spin-exchange rates are near to the SE prediction, the semblance of hydrodynamic behavior is superficial and arises incidentally from mathematical cancellation of terms in a generalized diffusion coefficient. As a collision pair coexists for a time within a solvation shell, the recollision time places a lower limit on the lifetime of the solvent cage. Although molecular dynamics simulations conducted thus far have yielded cage lifetimes lower than the measured recollision times, this is attributable to the fact that such simulations have mostly examined cage configurations too small to harbor a spin-exchange encounter, and is also likely due to restrictive mathematical definitions of cage lifetimes that are employed in such simulations.

Derivation of an empirical potential for gold with angular corrections

From a detailed analysis of density-functional calculations on gold model clusters and surfaces, an empirical potential for gold, which includes angular corrections, is derived. This potential introduces higher-order nonlinear terms (specifically, the product dipole-quadrupole) that do not seem to have been previously used, but that are necessary to describe directionality effects in the gold-gold interaction. Preliminary tests show that the proposed empirical potential possesses novel features with respect to the existing ones, such as a strong tendency of small Au clusters toward cage configurations, and represents a good starting point for future investigations.

Effects of hydrogen hosting on cage structures of boron clusters: density functional study of BmHn (m= 5–10 and n⩽m) complexes

The structural stability of hydrogen bonded boron microclusters has been studied by using the density functional theory. Effects of the increasing number of hydrogen atoms on the cage geometries of B5–B10 clusters, and the distortion of the cage configurations of the boranes are assessed. The possible stable structures of BmHn (m=5–10 and n⩽m) boron hydrides, their binding energies, HOMO–LUMO energy gaps and the total atomic charges of the Bm in the complexes are determined. For the series of B5Hn, B7Hn, and B9Hn major structural changes are observed.

The Dorsomedial Hypothalamic Nucleus Is Not Necessary for the Expression of Circadian Food-Anticipatory Activity in Rats

Restricted daytime feeding generates food-anticipatory activity (FAA) by entrainment of a circadian pacemaker separate from the light-entrainable pacemaker located in the SCN. The dorsomedial hypothalamic nucleus (DMH) has been proposed as the site of food-entrainable oscillators critical for the expression of FAA, but another study found no effects of complete DMH ablation on FAA. To account for these different results, the authors examined methodological factors, including (1) cage configuration and feeding method and (2) use of social cues. Intact and DMH-ablated rats were maintained on one 4-h daily meal in the middle of the light period, using caging and feeding methods matching those of Gooley et al. (2006). Rats with partial or complete DMH ablation were less nocturnal during ad lib food access but exhibited normal FAA during restricted feeding, as quantified by FAA magnitude, ratios, latency to appearance, duration, and precision. To evaluate the use of social cues, intact rats naive to restricted-feeding schedules were food deprived for 72 h on 4 tests. Daytime activity increased during food deprivation, but the magnitude and waveform of this activity was not influenced by the presence of food-entrained rats exhibiting robust FAA in adjacent cages. Thus, hungry intact rats do not use social cues to anticipate a daily mealtime, suggesting that DMH-ablated rats do not anticipate meals by reacting to sounds from food-entrained intact rats in adjacent cabinets. These results confirm our previous finding that the DMH is not critical for normal expression of FAA in rats, and this observation is extended to food restriction methodologies used by other labs. The methodological differences that do underlie discrepant results remain unresolved, as does the location of food-entrainable oscillators, input pathways, and output pathways critical for FAA.

Self-Interstitial in Germanium

Low-temperature radiation damage in n- and p-type Ge is strikingly different, reflecting the charge-dependent properties of vacancies and self-interstitials. We find, using density functional theory, that in Ge the interstitial is bistable, preferring a split configuration when neutral and an open cage configuration when positively charged. The split configuration is inert while the cage configuration acts as a double donor. We evaluate the migration energies of the defects and show that the theory is able to explain the principal results of low-temperature electron-irradiation experiments.

Lowest-energy endohedral fullerene structure ofSi60 from a genetic algorithm and density-functional theory

The lowest-energy structure of theSi60 cluster has been determined from an unbiased search using a genetic algorithm(GA) with the tight-binding model followed by local optimization of ‘hand-made’structures using density-functional theory (DFT). GA simulations show thatSi60 tends to adopt endohedral fullerene configurations. A large number ofisomers with different stuffing/cage ratio and cage configuration werethen constructed and optimized at DFT level. An endohedral fullerene ofSi12@Si48 was found to be most stable; it is energetically preferred to the hollowIh cage by 12.371 eV and to a previously proposed lowest-energy structure by4.841 eV. The competition between different structural growth patterns atSi60 is discussed.

Dual Relationship Between Large Gold Clusters (Antifullerenes) and Carbon Fullerenes: A New Lowest‐Energy Cage Structure for Au50.

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Dual Relationship between Large Gold Clusters (Antifullerenes) and Carbon Fullerenes: A New Lowest-Energy Cage Structure for Au50

Recent theoretical prediction and experimental confirmation of cage configurations for Au clusters have stimulated considerable interest in finding novel gold clusters exhibiting high stability. We use a dual relationship between gold antifullerene cages with all triangular faces and carbon fullerenes with all degree 3 vertices to construct a large number of Au50 antifullerene cages by omnicapping and dualization procedures. Among these cages we find a new D6d cage as the lowest-energy configuration of Au50. The unusual stability of this new Au50 cage is associated with spherical aromaticity and sp-d hybridization.

Pore Structures of Ordered Large Cage-Type Mesoporous Silica FDU-12s

The pore variations of ordered cage-type mesoporous silica FDU-12s have been analyzed in detail by PXRD, SAXS, nitrogen sorption, and electron crystallography. FDU-12s with a cubic symmetry (space group, Fmm) were templated by amphiphilic triblock copolymer F127 with the addition of 1,3,5-trimethylbenzene and KCl under an acidic condition. Three typical samples with different unit cell sizes, pore cage diameters, and entrance sizes were obtained from different synthesis and hydrothermal treatment temperatures, as indicated by the differences in the PXRD and SAXS patterns. The pore structure changes in the three materials were observed by nitrogen adsorption/desorption and 3-D reconstruction of HRTEM images taken from different crystal orientations. The approximate pore structures of FDU-12s can be regarded as a face-centered cubic (fcc) close-packing of spherical cages, each connected to 12 nearest neighboring cages. However, the ideal spherical model is only valid for the FDU-12s prepared at a low temperature (L-FDU-12-100). The cage shape of the FDU-12s synthesized at a high temperature deviates from perfect spheres and is accompanied by an entrance enlargement. The temperature-dependent behavior of the PEO block is discussed with regard to its influence on the micelles and hence the cage configuration. The better understanding of the formation mechanism via the combined characterization techniques and modeling may lead to a more rational approach for tuning the pore cages and entrances of the mesoporous FDU-12 materials.

The Effect of Interbody Cage Positioning on Lumbosacral Vertebral Endplate Failure in Compression

A biomechanical investigation using a human cadaver, multisegmental lumbosacral spine model. To determine if 2 small, posterolaterally positioned titanium mesh interbody cages would provide superior construct strength and stiffness in compression compared to central cage placement. In addition, determine construct stiffness with interbody cages as opposed to an intact spine and assess the effect of bone mineral density (BMD). Previous work has shown that the posterolateral corners of the lumbosacral endplates are stronger than the anterior and central regions. Information to suggest appropriate interbody cage positioning to avoid subsidence into adjacent vertebrae would be valuable for spine surgeons and implant designers. A total of 27 functional spinal units from L3 to S1 were dual x-ray absorptiometry scanned for BMD, instrumented with pedicle screw systems, and tested to failure in compression with titanium mesh interbody cages placed in 1 of 3 positions: 2 small posterolateral, 2 small central, or 1 large central. Analysis of covariance was conducted to compare failure load and stiffness across the different cage configurations. Repeated measures analysis of variance was used to analyze stiffness between functional spinal units with intact disc, discectomy, or interbody cages. Failure load was correlated against BMD. Of the 3 placement patterns, 2 small titanium mesh cages in the posterolateral corners had 20% higher failure loads, although the difference was not significant (P = 0.20). Stiffness in compression for the 3 cage positions was not significantly different (P = 0.82). All intact discs with posterior instrumentation were significantly stiffer than any of the cage patterns (P = 0.0001). BMD of the vertebrae significantly correlated with failure loads (P = 0.007). The placement of 2 small interbody cages posterolaterally tended to result in higher failure loads than central cage placement, although the results were not statistically significant. It is noteworthy that cage placement in any position resulted in a less stiff construct in compression than with an intact disc.

Hollow Cages versus Space-Filling Structures for Medium-Sized Gold Clusters: The Spherical Aromaticity of the Au50 Cage

Candidates for the lowest energy structures of medium-sized Au(n), n = 32, 38, 44, 50, and 56, clusters were evaluated using gradient-corrected DFT computations. Both hollow cage and space-filling conformations were considered. The cages were constructed using fullerene-based templates. The space-filling structures were generated by employing a genetic algorithm. We have found that the space-filling isomers were lower in energy except for two notable cases. Like Au(32) [Johansson, M. P.; Sundholm, D.; Vaara, J. Angew. Chem. Int. Ed. 2004, 43, 2678], a hollow cage configuration of Au(50) is more stable than its alternative space-filling isomeric forms. The unusual stabilities of the cage Au(32) and Au(50) can be attributed to spherical aromaticity; both exhibit large negative nucleus-independent chemical shifts and exceptionally large HOMO-LUMO gaps.

Structure-property relationships of hydrido organo siloxane polymer (HOSP)

The structure and properties of Hydrido Organo Siloxane Polymer (HOSP) as a function of cure conditions have been analyzed. Fourier transform infrared spectroscopy, dielectric constant, and mechanical properties all indicated a dependence on the bake sequence of HOSP. FT-IR analysis indicated that the ratio of Si-O bonds in a caged (or ordered) configuration to Si-O bonds in a non-caged (or disordered) configuration changed as a function of both pre-cure hot plate bake conditions and cure temperature. The dielectric constant was lower for samples that received a high temperature hot plate bake (400°C) prior to the furnace cure independent of the furnace cure temperature, compared with samples that did not undergo the high temperature hot plate bake. In addition, adhesion was significantly improved with an increase in the cure temperature from 400°C to 430°C. These results indicate that both pre-cure hot plate bake conditions, and cure temperature affect the structure and therefore the properties of HOSP. Optimum properties are achieved when both the 400°C hot plate bake and a 430°C furnace cure are employed.

Structure and Thermodynamics of H+(H2O)n (n = 9, 21, 40) Clusters between 0 and 300 K. A Monte Carlo Study

We present a Monte Carlo study of protonated water clusters, H+(H2O)n, with size n = 9, 21, and 40, and neutral clusters, (H2O)20, in the temperature range 0 to 300 K. We study the structural differences between the solidlike and liquidlike phases, using an empirical polarizable water model. The transition between these two phases is particularly distinct in H+(H2O)21, which attains the dodecahedral cage configuration at temperatures up to 150 K, a structure that does not survive above 170 K. The results support the idea that the “magic number” behavior of H+(H2O)21 is restricted to temperatures below the melting point. We estimate the melting temperatures for H+(H2O)9, H+(H2O)21, and (H2O)20 as predicted by the model to be 130, 160, and 160 K, respectively. The melting process in the protonated clusters thus appears to be governed mainly by water−water interactions.

Ab initio study of C 20 isomers: geometry and vibrational frequencies

Geometry optimizations are performed for three isomers of C 20, namely the ring, bowl (corannulene-like), and cage (fullerene-like) configurations, using both the local density functional approximation (LDA), and gradient-corrected density functional theory (BLYP). The BLYP results confirm the previous single point calculation based on Hartree-Fock geometries, which is in favor of the ring geometry, while the LDA results still indicate a reversed order of energy, thus favoring the cage geometry. Our calculated LDA vibrational spectra of the ring geometry show significant differences with those of HF in the widths of two band gaps. In addition, our Møller-Plesset second-order perturbation theory (MP2) single point calculations using GAMESS show preference towards the bowl structure, which differs from previous similar calculations.

An Aquatic Cage Design for Evaluating Exposure Routes in in Situ Xenobiotic Studies

Abstract We designed and constructed two all-plastic enclosures suitable for caging 50 juvenile channel catfish (Ictalurus punctatus) for in situ studies. The basic design allows caged organisms to come in contact with both sediment and water, but it can be easily altered to produce a cage that allows no contact between organisms and sediment. Both cage configurations were tested in the field and were found to be practical and durable.

Effects of Cage Population on the Productive Performance of Layers

Two commercial layer strains (3,456 hens total) were used to examine the effects of bird population on productive performance. Four cage population sizes (6, 8, 12, and 24 birds per cage) were compared. All cages were 35.7 cm deep and varied in width (61.2, 81.6, 122.4, and 244.8 cm). Floor space per bird was 364.1 cm2 and feeder space per bird was 10.2 cm in each cage configuration. Egg production and egg quality were measured from 20 to 72 wk of age. Strain differences were detected in hen-day egg production, egg mass, feed consumption, cracked egg percentage, Grade A eggs, Grade B eggs, peewee eggs, and large egg yield. There were no interactions between strain and cage population size. Cage population had no influence on hen-day egg production, mortality, feed conversion, egg size (peewee, small, medium, large, extra large), egg mass, lost eggs (by meat or blood spots), and percentage Grade B eggs. Percentage Grade A eggs, cracked egg percentage, and feed consumption were significantly influenced by cage population size. Hens housed at eight birds per cage had a greater percentage of Grade A eggs and a lower percentage of cracked eggs than those at other populations. Feed consumption was significantly greater for hens housed at 12 and 24 birds per cage compared with those at 6 and 8 birds per cage, respectively.