Detection of errors in dinucleotide repeat typing by nondenaturing electrophoresis.

This study shows that consideration of minor bands (heteroduplex, shadow, and faint bands) associated with allele bands in nondenaturing polyacrylamide gel electrophoresis (PAGE) after polymerase chain reaction (PCR) is effective for detecting PCR processing errors that lead to mistyping of heterozygotes as homozygotes. Notably, we show that minor bands in native gels are highly effective for detecting allele dropout and preferential amplification in PCR amplification of dinucleotide repeats. These findings are based on an analysis of Mendelian inheritance patterns in families, and the reproduction of heterozygous band patterns by mixing homozygous DNAs before PCR, for a total of six (AC)n repeats located on human chromosome 11p15. To investigate the utility of our approach, a large population sample of 405 unrelated individuals was genotyped for each (AC)n repeat using minor bands as internal quality controls. Genotype frequencies at each of the six loci were in close agreement with Hardy-Weinberg proportions, which suggests that there were few genotyping errors. Our observations add to the evidence indicating that minor bands in native gels are of diagnostic value in the genotyping of dinucleotide repeats.     

Uncoupled peptide bond vibrations in alpha-helical and polyproline II conformations of polyalanine peptides

We examined the 204-nm UV resonance Raman (UVR) spectra of the polyproline II (PPII) and alpha-helical states of a 21-residue mainly alanine peptide (AP) in different H2O/D2O mixtures. Our hypothesis is that if the amide backbone vibrations are coupled, then partial deuteration of the amide N will perturb the amide frequencies and Raman cross sections since the coupling will be interrupted; the spectra of the partially deuterated derivatives will not simply be the sum of the fully protonated and deuterated peptides. We find that the UVR spectra of the AmIII and AmII' bands of both the PPII conformation and the alpha-helical conformation (and also the PPII AmI, AmI', and AmII bands) can be exactly modeled as the linear sum of the fully N-H protonated and N-D deuterated peptides. Negligible coupling occurs for these vibrations between adjacent peptide bonds. Thus, we conclude that these peptide bond Raman bands can be considered as being independently Raman scattered by the individual peptide bonds. This dramatically simplifies the use of these vibrational bands in IR and Raman studies of peptide and protein structure. In contrast, the AmI and AmI' bands of the alpha-helical conformation cannot be well modeled as a linear sum of the fully N-H protonated and N-D deuterated derivatives. These bands show evidence of coupling between adjacent peptide bond vibrations. Care must be taken in utilizing the AmI and AmI' bands for monitoring alpha-helical conformations since these bands are likely to change as the alpha-helical length changes and the backbone conformation is perturbed.     

信号处理技术在重叠化学信号解析中的应用*

重叠峰解析是目前分析化学中亟须解决的一个重要问题,化学计量学用于重叠峰解析就是借助某些数学或统计学方法,把通过化学方法和仪器未能完全分离的复合量测信号分解成几个单儿组分的信号,从而从重叠谱中获取每个组分的相关信息。本文综述了几种常见信号处理技术在重叠化学信号分辨中的应用,引用文献146篇。     

Alkali and alkaline-earth ion vibrations in solvent cages,coordination compounds,glasses and related systems

Alkali metal ion—oxygen donor solvent cages as well as coordination compounds, alkali metal oxide glasses and oxyanion salts of alkali metals exhibit low-frequency bands in the infrared spectrum characteristic of the cation—oxygen polyhedra. Similar bands are seen with nitrogen donors. Alkaline earth ions also show such absorption bands due to quantised vibration of cations. These bands not only provide a means of establishing the nature of cation coordination in diverse systems, but also serve as probes to examine ion-solvent interactions.     

Chain orientation and distribution in ring‐banded spherulites formed in poly(ester urethane) multiblock copolymer

A poly(ester urethane) multiblock copolymer containing poly(ε‐caprolactone) glycol (PCL) soft segments gives ring‐banded spherulite as crystallized from its melted film. Analysis based on polarized light microscopy and atomic force microcopy revealed that the ring‐banded structures consist of alternate convex and concave bands as a consequence of rhythmic growth. These convex and concave bands, which are composed of flat‐on and edge‐on lamellae, show layered terrace‐like and fibrillar morphology, respectively. The chain orientation and composition distribution in the ring‐banded spherulites were further investigated using FTIR imaging. The convex bands are mainly PCL‐rich domains with perpendicular chain orientation to the substrate, and the concave bands are urethane‐rich domains, where the PCL chains are perpendicular to the radial growth directions of the spherulite but parallel to the film plane. The formation of different orientations in the convex and concave bands is attributed to the rhythmic growth behavior for the copolymers with composition distribution along the chains. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 541–547, 2010     

Experimental study of the dynamics of front propagation in the Co(OH)2/NH4OH Liesegang system using spectrophotometry

In this paper we study the temporal dynamics of the Co(OH) 2/NH 4OH Liesegang system with redissolution by complex formation with ammonia using UV-vis spectrophotometry with a special setup. The formation of precipitate bands is accompanied with band redissolution at the top, and because of such precipitation-redissoultion dynamics, the bands appear as a propagating wave. The spectrophotometric technique developed in this study allows us to study at the kinetics of formation of the bands and their redissolution in great details. The formation, growth, and dissolution of multiple bands are monitored by the time evolution of the absorbance. It was found that the individual band formation is sudden and takes between 15 min to half an hour to form before the next band appears. The speed of formation of bands was different for different bands and the maxima of these speeds fit a Gaussian curve. The content of cobalt hydroxide in these bands was calculated and is shown to increase to a maximum away from the interface and then decreases. The bands later grow by further precipitation. This growth was demonstrated to be nonlinear in time. On the other hand, the dissolution of bands was shown to take place simultaneously and collectively among the multiple bands under study. The effect of the concentration of Co (+2) ions on the dynamics of band formation and dissolution was studied. A time law for this Liesegang system was also determined. The system was also found to be very sensitive to temperature fluctuations.     

Structural basis for the discrepancy of spectral behavior in C-H stretching band between steroids and long chain hydrocarbon compounds

The discrepancies of the spectral behavior for the C-H stretching band between some long chain hydrocarbon compounds and steroids were investigated. At low temperature, the C-H stretching bands exhibit complex fine structure in steroids but remain simple in long chain hydrocarbon compounds. MM3 molecular mechanics calculation indicates that, for long chain hydrocarbon compounds, the C-H groups vibrate with large scale coupling. There exist a few bands where the C-H groups vibrate in synchronous and inphase mode. Thus the variations of dipole moment for these bands are enhanced and the intensities are obviously stronger than others and cover other band in the spectra. This is just the reason why the C-H stretching bands are simple even at low temperature environment. Nevertheless, for the steroids, the C-H stretching bands vibrate with local coupling mode. The synchronous enhancement effect does not occur, the differences of intensities for various modes are not as large as those in long chain hydrocarbo     

Characterization and promotion of dilatation bands in toughenable thermosetting resins

Formation of dilatation bands has been found in a series of moderately crosslinked thermosets with molecular weights between crosslinks, Mc, ranging from 560 to 1000 g/mole. These dilatation bands, although they do not show distinct craze fibrils inside the band, do behave mechanically like the well-known crazing phenomenon observed in polystyrene. Although the cause for the formation of dilatation bands is still largely unknown, the occurrence of the craze-like fracture phenomenon (dilatation bands) is found to be strongly influenced by the stress state the matrix experiences, by the type of loading applied to the specimen, and by the type/size of toughener particles incorporated in the matrix. The tendency for dilatation band formation in engineering thermosets can be greatly enhanced by the use of craze-prone toughener particles, such as nylon particles. The toughening effect via these newly observed dilatation bands is found to be quite impressive, and in some cases, can approach that via the shear-banding process. The potential significance of the present finding for a better design of toughened thermosets for structural applications is discussed. ©1995 John Wiley & Sons, Inc.     

The application of schlieren optics for detection of protein bands and other phenomena in polyacrylamide gel electrophoresis

A modernized schlieren optics system was applied to follow protein bands visually during polyacrylamide gel electrophoresis. This approach is suitable for quantitative measurement of electrophoresis as well as for detection of protein bands because of the absence of distortion of the electrophoretic pattern during the staining process. The optics are also suitable for the detection of various background phenomena which usually escape observation.     

Shear bands in polycarbonate

Lexan polycarbonate specimens in the form of tubes were deformed in torsion. The deformation occurs by the nucleation and growth of discrete shear bands. Shear bands are initially formed at the upper yield point. Development of the bands is accompanied by a drop in the stress to a lower yield point. At the lower yield point the strain inside the bands is approximately 70% and remains constant thereafter. Further deformation occurs by growth of the bands until they cover the entire sample. When the direction of twisting is reversed after the shear bands are formed, the deformed material untwists uniformly, without deformation in the previously undeformed material, and the stress required for untwisting the deformed material is lower than the stress required to propagate the band into undeformed material.     

The growth of shear bands in polystyrene

Shear-band growth velocities have been determined as a function of stress and temperature in polystyrene. The results demonstrate that shear bands can propagate under isothermal conditions; an adiabatic temperature rise at the shear band tip is not necessary for continued localization and growth of the band. The velocity is stress activated with a shear activation volume of 4600 ų and thermally activated with an activation enthalpy of 2.8 eV. Comparison of these values of the activation parameters with those for bulk shear flow in polystyrene indicates that the shear band propagation is controlled by the plastic strain rate of the glassy polymer immediately ahead of the tip of the band. Argon's molecular kink model of the elemental deformation process is consistent with measured values of the activation parameters whereas Bowden and Raha's dislocation model is not. The shear bands grow at an angle of ca. 38° to the axis of compression, and if the direction of compression is altered, the shear bands will change direction so as to maintain the 38° angle. Current explanations can not quantitatively account for the large deviation of the shear bands from the 45° plane of maximum shear stress.     

Time-dependent fifth-order bands in nominally third-order 2D IR vibrational echo spectra

Progress in the field of 2D IR vibrational spectroscopy has been bolstered by the production of intense mid-IR laser pulses. As higher-energy pulses are employed, a concomitant increase occurs in the likelihood of fifth-order contributions to the 2D IR spectra. We report the appearance of fifth-order signals in 2D IR spectra of CO bound to the active site of the enzyme cytochrome P450(cam) with the substrate norcamphor. Two bands with novel time dependences, one on the diagonal and one off-diagonal, are not accounted for by normal third-order interactions. These bands are associated with a ν = 1-2 vibrational transition frequency. Both bands decay to 0 and then grow back in with opposite sign. The diagonal band is positive at short time, decays to 0, reappears with negative sign, before eventually decaying to 0. The off-diagonal band is negative at short time, decays to 0, reappears positive, and then decays to 0. The appearance and time dependence of these bands are characterized. Understanding these fifth-order bands is useful because they may be misidentified with time-dependent bands that arise from other processes, such as chemical exchange, vibrational coupling, or energy transfer. The presence and unusual time dependences of the fifth-order bands are reproduced with model calculations that account for the fact that vibrational relaxation from the ν = 2 to 1 level is approximately a factor of 2 faster than that from the ν = 1 to 0 level.     

Application of time-domain differentiation of chromatographic peaks in liquid chromatography

The differentiation of chromatographic bands with respect to time is useful for improving the resolution of overlapping peaks owing to the reduced band widths of derivatives in comparison with the original bands. An IBM XT 286 microcomputer was interfaced to a Perkin-Elmer liquid chromatographic system and software was developped to allow the acquisition and digitization of chromatographic data for subsequent manipulation, storage and graphical representation. Smoothing and differentiation of chromatographic bands with respect to time were done by the Savitzky-Golay method. The method was applied to the determination of a mixture of antioxidants used as additives in nutrition. The overlapping peaks corresponding to propyl gallate and tert-butylhydroquinone were resolved by time-domain differentiation.     

Fourier self-deconvolution in IR spectroscopy

Fourier self-deconvolution (FSD) is a mathematical means for reducing bandwidths, so that overlapped bands can be resolved from one another. The principles of FSD are described briefly, and examples are shown of how overlapped infrared spectra can be enhanced so as to greatly improve their information content. The disadvantages of FSD are discussed and it is shown how the method can be extended to extract individual components from a composite envelope of bands.     

Solvation of GaCl3 in deuterated acetonitrile studied by means of vibrational spectroscopy

Remarkably large blue shifts of the nu2 C [triple bond] N stretch, nu4 C-C stretch, and nu8 CCN deformation bands of CD3CN are observed in the infrared and Raman spectra of CD3CN solution of GaCl3, resulting from the donor-acceptor interaction of CD3CN with the Lewis acid. The Raman spectrum in the nu2 region shows further details; three new bands emerge on the blue side of the nu2 band of free CD3CN and the relative intensities between the bands vary with concentration, suggesting that there exist at least three different complexes in the solution. Parallel to the nu2 region, similar new bands are observed on the blue sides of the nu4 and nu8 bands of free CD3CN. The strong hydrogen bonds formed between the CD3 group and the chlorine atoms of the solute result in a large band appearing on the low frequency side of the nu1 CD3 symmetric stretch band of free CD3CN. The solvation number of GaCl3, as determined from the Raman intensities of the C [triple bond] N stretch bands for free and coordinated CD3CN, increases from 1.3 to about 1.7 with decreasing concentration.     

Far-infrared studies of alkali-anthracene ion-pairs and triple-ions in solution

Solutions of the anthracene mono- and di-anion produced by reduction with alkali metals in tetrahydrofuran show absorption bands in the far-infrared region. These bands have been interpreted as arising from the vibration of ion-pairs and triple-ions. The corresponding force constants have been calculated using simple models. Some discussions is given of possible causes of the two absorption bands of the sodium-anthracene triple-ion.     

Immunochromatographic removal of albumin in erythropoietin biopharmaceutical formulations for its analysis by capillary electrophoresis

Human serum albumin (HSA) is added to some pharmaceutical preparations as an excipient. This is the case for some of the commercial preparations of recombinant erythropoietin (rEPO). Differences in the number of the sialic acid moieties in the different rEPO glycoforms confer to these forms different net charges and different bioactivity. Knowledge of the isoforms present in each pharmaceutical product is then of interest. Differences in net charge of the rEPO forms make possible their separation by electrophoretical methods. However it has been observed in our laboratory that the amount of HSA usually present in these drug formulations interferes or even precludes separation of rEPO bands by capillary zone electrophoresis (CZE). In this work, an immunochromatographic method to remove HSA from rEPO biopharmaceutical formulations and a procedure to concentrate the sample that is needed to be performed prior to the analysis by CZE are developed. A home-made computer program to compare the percentage of correct assignments of electrophoretical bands provided by different migration parameters is used to study the effect of HSA remaining in samples on the accuracy of assignment of rEPO bands. When there exists a residual concentration of HSA in the sample (<2mg/ml) only the effective electrophoretic mobility is a reliable migration parameter to assign rEPO bands with a 100% of correct assignment. This parameter allows the correct assignment of bands of rEPO from pharmaceutical products formulated with HSA after immunochromatographic removal of HSA. Electrophoretical bands found in epoetin alpha, one of the commercial formulations of rEPO, are independent of the molecular mass of the excipients. The methodology used in this work for the analysis by CZE and the assignment of rEPO isoforms, as well as for the immunochromatographic HSA removal in the pharmaceutical products could be of high interest for the health authorities to control the quality of the product in marketing surveillance studies and for the quality control laboratories of the manufacturers.     

Optical absorption of tetraphenylporphyrin thin films in UV-vis-NIR region

The optical absorption of thermally evaporated tetraphenylporphyrin (TPP) in the UV-vis-NIR region have been studied. The absorption spectra recorded in the UV-vis region for the as deposited and annealed films showed different absorption bands, namely the Soret(B) at region 360-490nm, Q-band region consist of four bands in the region 500-720nm and two other bands labeled N and M in UV region. The Soret band always shows its characteristic effect splitting in all the TPP thin films and the effect of annealing on the intensities of these components have been observed. The spectra of the infrared absorption allow characterization of vibrational modes for the powder, as deposited and annealed thin films. Some of the optical absorption parameters, namely molar extinction coefficient, varepsilon, half band width, Deltalambda, electronic dipole strength, q(2) and oscillator strength, f, of the principle optical transitions have also been evaluated.     

Simple methods for assessing the conformational sensitivity of infrared bands by dichroism

In characterizing the overall orientation of polymers by infrared (IR) dichroism, the orientation function must be obtained from the dichroic ratios of conformationally insensitive bands. Identification of such bands is thus necessary prior to the calculation of the orientation function. In this study, we devise two simple methods for evaluating the conformational sensitivities of IR bands from the measurement of the dichroic ratio. Both methods are based on the fact that the orientation function calculated by all conformationally insensitive bands should be identical, while this is not true for conformationally sensitive bands. Poly(ether ether ketone) (PEEK) is used as an example to demonstrate the use of these methods.