Investigation of DMSO-Induced Conformational Transitions in Human Serum Albumin Using Two-Dimensional Raman Optical Activity Spectroscopy

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Two-Dimensional Crystallisation of Membrane Proteins and Structural Assessment

Two-dimensional (2D) crystallisation of Membrane proteins reconstitutes them into their native environment, the lipid bilayer. Electron crystallography allows the structural analysis of these regular protein–lipid arrays up to atomic resolution. The crystal quality depends on the protein purity, ist stability and on the crystallisation conditions. The basics of 2D crystallisation and different recent advances are reviewed and electron crystallography approaches summarised. Progress in 2D crystallisation, sample preparation, image detectors and automation of the data acquisition and processing pipeline makes 2D electron crystallography particularly attractive for the structural analysis of membrane proteins that are too small for single-particle analyses and too unstable to form three-dimensional (3D) crystals.

The two-dimensional IR nonlinear spectroscopy of a cyclic penta-peptide in relation to its three-dimensional structure

A form of two-dimensional (2D) vibrational spectroscopy, which uses two ultrafast IR laser pulses, is used to examine the structure of a cyclic penta-peptide in solution. Spectrally resolved cross peaks occur in the off-diagonal region of the 2D IR spectrum of the amide I region, analogous to those in 2D NMR spectroscopy. These cross peaks measure the coupling between the different amide groups in the structure. Their intensities and polarizations relate directly to the three-dimensional structure of the peptide. With the help of a model coupling Hamiltonian, supplemented by density functional calculations, the spectra of this penta-peptide can be regenerated from the known solution phase structure. This 2D-IR measurement, with an intrinsic time resolution of less than 1 ps, could be used in all time regimes of interest in biology.

Measuring The Hydrodynamic Radius Of Quantum Dots By Fluorescence Correlation Spectroscopy.

Fluorescence Correlation Spectroscopy (FCS) is an optical technique that allows the measurement of the diffusion coefficient of molecules in a diluted sample. From the diffusion coefficient it is possible to calculate the hydrodynamic radius of the molecules. For colloidal quantum dots (QDs) the hydrodynamic radius is valuable information to study interactions with other molecules or other QDs. In this chapter we describe the main aspects of the technique and how to use it to calculate the hydrodynamic radius of quantum dots (QDs).

Measurement Of The Hydrodynamic Radius Of Quantum Dots By Fluorescence Correlation Spectroscopy Excluding Blinking.

One of the most important properties of quantum dots (QDs) is their size. Their size will determine optical properties and in a colloidal medium their range of interaction. The most common techniques used to measure QD size are transmission electron microscopy (TEM) and X-ray diffraction. However, these techniques demand the sample to be dried and under a vacuum. This way any hydrodynamic information is excluded and the preparation process may alter even the size of the QDs. Fluorescence correlation spectroscopy (FCS) is an optical technique with single molecule sensitivity capable of extracting the hydrodynamic radius (HR) of the QDs. The main drawback of FCS is the blinking phenomenon that alters the correlation function implicating in a QD apparent size smaller than it really is. In this work, we developed a method to exclude blinking of the FCS and measured the HR of colloidal QDs. We compared our results with TEM images, and the HR obtained by FCS is higher than the radius measured by TEM. We attribute this difference to the cap layer of the QD that cannot be seen in the TEM images.

Two-dimensional radiographic and clinical references of the tooth crown for orthodontic mini-implant insertion: A guide-free technique

Objective. This study evaluated the reliability of tooth-crown radiographic references to aid in orthodontic mini-implant insertion and showed an insertion technique based on these references. Study design. The sample consisted of 213 interradicular septa evaluated in 53 bitewing radiographs. The proximal contour of adjacent tooth crowns was used to define septum width and its midpoint was linked to the interdental contact point to determine septum midline (SML). The distances from SML to mesial and distal teeth were measured and compared to evaluate SML centralization degree in 2 different septum heights. Results. The mesial and distal distances were not statistically different in the midpoint of the septum height, but they were different at the apical septum height. Conclusions. The tooth-crown radiographic references determine a high centralization degree of the SML on which an insertion site could be defined. The greater SML centralization degree was observed at the coronal septum area. (Oral Surg Oral Med Oral Pathol Oral Radiol Endod 2010;110:e8-e16)

Analysis of pesticide residues in strawberries and soils by GC-MS/MS, LC-MS/MS and two-dimensional GC-timeof- flight MS comparing organic and integrated pest management farming

This study analysed 22 strawberry and soil samples after their collection over the course of 2 years to compare the residue profiles from organic farming with integrated pest management practices in Portugal. For sample preparation, we used the citrate-buffered version of the quick, easy, cheap, effective, rugged, and safe (QuEChERS) method. We applied three different methods for analysis: (1) 27 pesticides were targeted using LC-MS/MS; (2) 143 were targeted using low pressure GC-tandem mass spectrometry (LP-GC-MS/MS); and (3) more than 600 pesticides were screened in a targeted and untargeted approach using comprehensive, two-dimensional gas chromatography time-of-flight mass spectrometry (GC × GC-TOF-MS). Comparison was made of the analyses using the different methods for the shared samples. The results were similar, thereby providing satisfactory confirmation of both similarly positive and negative findings. No pesticides were found in the organic-farmed samples. In samples from integrated pest management practices, nine pesticides were determined and confirmed to be present, ranging from 2 μg kg−1 for fluazifop-pbutyl to 50 μg kg−1 for fenpropathrin. Concentrations of residues in strawberries were less than European maximum residue limits.

Establishing two-dimensional gels for the analysis of Leishmania proteomes.

Several different sample preparation methods for two-dimensional electrophoresis (2-DE) analysis of Leishmania parasites were compared. From this work, we were able to identify a solubilization method using Nonidet P-40 as detergent, which was simple to follow, and which produced 2-DE gels of high resolution and reproducibility.

A two-dimensional doppler-radiometer for earth observation

Compared to synthetic aperture radars (SARs), the angular resolution of microwave radiometers is quite poor. Traditionally, it has been limited by the physical size of the antenna. However, the angular resolution can be improved by means of aperture synthesis interferometric techniques. A narrow beam is synthesized during the image formation processing of the cross-correlations measured at zero-lag between pairs of signals collected by an array of antennas. The angular resolution is then determined by the maximum antenna spacing normalized to the wavelength (baseline). The next step in improving the angular resolution is the Doppler-Radiometer, somehow related to the super-synthesis radiometers and the Radiometer-SAR. This paper presents the concept of a three-antenna Doppler-Radiometer for 2D imaging. The performance of this instrument is evaluated in terms of angular/spatial resolution and radiometric sensitivity, and an L-band illustrative example is presented.

Diagnostic performance of 3D TSE MRI versus 2D TSE MRI of the knee at 1.5 T, with prompt arthroscopic correlation, in the detection of meniscal and cruciate ligament tears

Abstract Objective: To compare the diagnostic performance of the three-dimensional turbo spin-echo (3D TSE) magnetic resonance imaging (MRI) technique with the performance of the standard two-dimensional turbo spin-echo (2D TSE) protocol at 1.5 T, in the detection of meniscal and ligament tears. Materials and Methods: Thirty-eight patients were imaged twice, first with a standard multiplanar 2D TSE MR technique, and then with a 3D TSE technique, both in the same 1.5 T MRI scanner. The patients underwent knee arthroscopy within the first three days after the MRI. Using arthroscopy as the reference standard, we determined the diagnostic performance and agreement. Results: For detecting anterior cruciate ligament tears, the 3D TSE and routine 2D TSE techniques showed similar values for sensitivity (93% and 93%, respectively) and specificity (80% and 85%, respectively). For detecting medial meniscal tears, the two techniques also had similar sensitivity (85% and 83%, respectively) and specificity (68% and 71%, respectively). In addition, for detecting lateral meniscal tears, the two techniques had similar sensitivity (58% and 54%, respectively) and specificity (82% and 92%, respectively). There was a substantial to almost perfect intraobserver and interobserver agreement when comparing the readings for both techniques. Conclusion: The 3D TSE technique has a diagnostic performance similar to that of the routine 2D TSE protocol for detecting meniscal and anterior cruciate ligament tears at 1.5 T, with the advantage of faster acquisition.

A two-dimensional X-ray scattering system for in-situ time-resolving studies of polymer structures subjected to controlled deformations

A two-dimensional X-ray scattering system developed around a CCD-based area detector is presented, both in terms of hardware employed and software designed and developed. An essential feature is the integration of hardware and software, detection and sample environment control which enables time-resolving in-situ wide-angle X-ray scattering measurements of global structural and orientational parameters of polymeric systems subjected to a variety of controlled external fields. The development and operation of a number of rheometers purpose-built for the application of such fields are described. Examples of the use of this system in monitoring degrees of shear-induced orientation in liquid-crystalline systems and crystallization of linear polymers subsequent to shear flow are presented.

Automated two-dimensional separation flow system with electrochemical preconcentration, stripping, capillary electrophoresis and contactless conductivity detection for trace metal ion analysis

This paper describes the automation of a fully electrochemical system for preconcentration, cleanup, separation and detection, comprising the hyphenation of a thin layer electrochemical flow cell with CE coupled with contactless conductivity detection (CE-C(4)D). Traces of heavy metal ions were extracted from the pulsed-flowing sample and accumulated on a glassy carbon working electrode by electroreduction for some minutes. Anodic stripping of the accumulated metals was synchronized with hydrodynamic injection into the capillary. The effect of the angle of the slant polished tip of the CE capillary and its orientation against the working electrode in the electrochemical preconcentration (EPC) flow cell and of the accumulation time were studied, aiming at maximum CE-C(4)D signal enhancement. After 6 min of EPC, enhancement factors close to 50 times were obtained for thallium, lead, cadmium and copper ions, and about 16 for zinc ions. Limits of detection below 25 nmol/L were estimated for all target analytes but zinc. A second separation dimension was added to the CE separation capabilities by staircase scanning of the potentiostatic deposition and/or stripping potentials of metal ions, as implemented with the EPC-CE-C(4)D flow system. A matrix exchange between the deposition and stripping steps, highly valuable for sample cleanup, can be straightforwardly programmed with the multi-pumping flow management system. The automated simultaneous determination of the traces of five accumulable heavy metals together with four non-accumulated alkaline and alkaline earth metals in a single run was demonstrated, to highlight the potentiality of the system.

Determination of potassium and sodium in an ash sample by gamma-ray spectroscopy

Neutron activation analysis and gamma-ray spectroscopy were used to determine the quantity of potassium and sodium in an ash sample of Tabebuia sp bombarded with thermal neutrons. These techniques, widely applied in nuclear physics, can be used in the context of wood science as an alternative for the usual physical chemistry methods applied in this area. The quantity of K and Na in an 8.60 +/- 0.10 mg of ash was determined as being 1.3 +/- 0.3 mg and 11.0 +/- 1.8 mu g, respectively. The ratio of Tabebuia sp converted into ash was also determined as 0.758 +/- 0.004%.

Self-Structuring of Lamellar Bridged Silsesquioxanes with Long Side Spacers

Diurea cross-linked bridged silsesquioxanes (BSs) C(10)C(11)C(10) derived from organosilane precursors, including decylene chains as side spacers and alkylene chains with variable length as central spacers (EtO)(3)Si- (CH(2))(10)-Y(CH(2))(n)-Y-(CH(2))(10)-Si(OEt)(3) (n = 7, 9-12; Y = urea group and Et = ethyl), have been synthesized through the combination of self-directed assembly and an acid-catalyzed sol gel route involving the addition of dimethylsulfoxide (DMSO) and a large excess of water. This new family of hybrids has enabled us to conclude that the length of the side spacers plays a unique role in the structuring of alkylene-based BSs, although their morphology remains unaffected. All the samples adopt a lamellar structure. While the alkylene chains are totally disordered in the case of the C(10)C(7)C(10) sample, a variable proportion of all-trans and gauche conformers exists in the materials with longer central spacers. The highest degree of structuring occurs for n = 9. The inclusion of decylene instead of propylene chains as side spacers leads to the formation of a stronger hydrogen-bonded urea-urea array as evidenced by two dimensional correlation Fourier transform infrared spectroscopic analysis. The emission spectra and emission quantum yields of the C(10)C(n)C(10) Cm materials are similar to those reported for diurea cross-linked alkylene-based BSs incorporating propylene chains as side spacers and prepared under different experimental conditions. The emission of the C(10)C(n)C(10) hybrids is ascribed to the overlap of two distinct components that occur within the urea cross-linkages and within the siliceous nanodomains. Time-resolved photoluminescence spectroscopy has provided evidence that the average distance between the siliceous domains and the urea cross-links is similar in the C(10)C(n)C(10) BSs and in oxyethylene-based hybrid analogues incorporating propylene chains as side spacers (diureasils), an indication that the longer side chains in the former materials adopt gauche conformations. It has also allowed us to demonstrate for the first time that the emission features of the urea-related component of the emission of alkylene-based BSs depend critically on the length of the side spacers.