Classification of Rhizoma et Radix Notoperygii by HPLC Fingerprints with the Aid of Chemometrics

Chromatographic profiles of Rhizoma et Radix Notoperygii (RRN, “Qianghuo” in Chinese), a complex traditional Chinese medicine (TCM), were collected by high-performance liquid chromatography with diode array detection (HPLC-DAD) at 330 nm. These data profiles were used as fingerprints to investigate quality control classification modeling of the RRN samples. In contrast to the classical methods for discrimination of TCMs, that is, just using common HPLC peaks, all chromatographic profile data were pre-processed by the correlation optimized warping method and polynomial functions; then, these data were submitted as fingerprints (variables) for classification on the basis of sample origin. Chemometrics methods used for calibration modeling and subsequent sample classification-least square support vector machine (LS-SVM), artificial neural network (ANN), and partial least square discriminant analysis (PLS-DA); all produced satisfactory calibrations as well as classification results.     

Proteomic analysis of laser capture microdissected human prostate cancer and in vitro prostate cell lines

Specific populations of normal and malignant epithelium from three radical prostatectomy tissue specimens were procured by laser capture microdissection (LCM) and analyzed by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). Six proteins that were only seen in malignant cells and two proteins that were only seen in benign epithelium were reproducibly observed in two of two cases examined. Furthermore, these proteins were not observed in the 2-D PAGE profiles from the patient-matched microdissected stromal cell populations, but were seen in the protein profiles from the undissected whole cryostat sections. One of these proteins was determined to be prostate-specific antigen (PSA) by Western blot analysis, and intriguingly the remaining protein candidates were found to be at least as abundant as the PSA protein. Comparison of 2-D PAGE profiles of microdissected cell with matched in vitro cell lines from the same patient, and metastatic prostate cancer cell lines (LnCaP and PC3) showed striking differences between prostate cells in vivo and in vitro with less than 20% shared proteins. The data demonstrate that 2-D PAGE analysis of LCM-derived cells can reliably detect alterations in protein expression associated with prostate cancer, and that these differentially expressed proteins are produced in high enough levels which could allow for their clinical utility as new targets for therapeutic intervention, serum markers, and/or imaging markers.     

The application of NIR Raman spectroscopy in the assessment of serum thyroid-stimulating hormone in rats

Serum blood samples of euthyroid and thyroidectomized rats treated with thyrotropin-releasing hormone (TRH) were analyzed on aluminum substrates using the near-infrared Raman spectroscopy (830 nm). Spectra of thyroid-stimulating hormone (TSH), TRH and prolactin standards were obtained. Differences between Raman spectra profiles of control and Tx + TRH samples groups were found. These differences were confirmed by the linear discriminant analysis (LDA), which presents a good classification between groups. It is supposed that these differences are produced by the increment of TSH in the thyroidectomized rats.     

Generation of linear and non-linear concentration gradients along microfluidic channel by microtunnel controlled stepwise addition of sample solution

The ability to generate stable chemical gradients in microfluidics has important applications, since such gradients are useful in both chemical and biological studies. Growing evidence reveals that many cellular responses are specific to non-linear spatial gradients, hence a need to control complex concentration gradient profiles with and within microfluidics. In this paper, we present a structure-based approach to generate linear and non-linear chemical gradients, with profiles controlled by microtunnels fabricated alongside two main channels. Using single-step photolithography, microtunnels and main channels were fabricated at different heights thus having different fluidic resistance. Through these microtunnels, sample solutions were stepwise dispensed into the buffer stream to generate a chemical gradient profile. By varying the lengths of microtunnels that dictated the volume of sample solutions being dispensed, complex gradient profiles were generated. We have successfully demonstrated the formation of linear, convex and concave gradient profiles and a simple mathematical expression was established to approximate the profiles produced in our microfluidic gradient-generators.     

Mapping concentration profiles within the diffusion layer of an electrode: application to redox catalysis

Catalytic reductions of some aromatic halides were performed at a millimetric electrode with several redox mediators. The resulting concentration profiles were monitored amperometrically by placing an ultramicroelectrode inside the diffusion layer produced at the former electrode. The features of redox catalysis and the subsequent structuring of the diffusion layer were investigated experimentally under steady-state conditions imposed by the spontaneous convection of the solution. The concentration profiles established from the probe measurements were in agreement with our theoretical predictions, based on fast kinetics of redox catalysis. Under these conditions, very similar to preparative electrosynthesis, the diffusion layer separates into two domains where pure diffusion takes place and the concentration profiles therein are mainly linear. We demonstrate that the limit between these two zones does not depend on kinetics, but is rather fixed by the product of the ratio of the bulk concentrations of each species and the ratio of their diffusion coefficients.     

High-throughput profiling of N-linked oligosaccharides in therapeutic antibodies using a microfluidic CD platform and MALDI-MS

Recombinant therapeutic antibodies have shown a great potential in the treatment of several severe medical conditions such as cancer and autoimmune diseases. Glycosylation plays a critical role in biological activity and immunogenic properties of these compounds. The analysis of glycan profiles is therefore necessary in many steps of the development and manufacturing process from early development to quality control of the final product. In this paper, a fast, parallel, and robust sample preparation platform for glycosylation profiling using a microfluidic compact disc (CD) is presented. A sequential process including selective capture of antibody from a crude cell supernatant using protein A beads, enzymatic release of glycans, purification with a graphitized carbon black column, and crystallisation for MALDI-TOF analysis were performed on the CD. Glycosylation profiles of an antibody intended for therapeutic use produced in two different cell lines were compared.     

Determination of the enantiomerization barrier of thalidomide by dynamic capillary electrokinetic chromatography

Enantioselective chromatographic methods, representing the most commonly used techniques for the determination of enantiomeric ratios, can also be used for the evaluation of stereochemical integrity. In the present study, dynamic capillary electrokinetic chromatography (DEKC) was employed to determine the enantiomerization barrier of thalidomide. In the presence of the chiral mobile phase additive carboxymethyl-beta-cyclodextrin, the interconverting enantiomers of thalidomide produced characteristic elution profiles exhibiting plateaus and/or peak broadening between 25 and 55 degrees C at pH 8. To obtain the enantiomerization barrier of thalidomide from experimental data, the fast and efficient simulation program ChromWin was used to simulate the experimental interconversion profiles and to obtain the apparent rate constants k1app(T). Additionally, these values were compared with the novel approximation function for the direct calculation of enantiomerization barriers from chromatographic parameters of elution profiles. From the rate constants k1app(T) of temperature-dependent measurements the kinetic activation parameters deltaG(T)#,deltaH#, and deltaS# of the enantiomerization of thalidomide were obtained. At 25 degrees C, the enantiomerization barrier deltaG# was determined to be 102 +/- 1 kJ/mol at pH 8 in the dynamic electrokinetic chromatographic experiment.     

Analysis of a photosensitive lesion induced by sunlamp UV greater than 315 nm exposure of 254-nm-irradiated human cells

Normal human skin fibroblasts were exposed to 0-10 J m-2 of 254 nm UV, incubated 0-16 h and then treated with 0-150 kJ m-2 of sunlamp UV greater than 315 nm. For each treatment, the cells were subjected to alkaline elution in order to measure the yield of single strand breaks (ssb) produced. It was found that treatment of 254-nm-irradiated cells with sunlamp UV greater than 315 nm resulted in the production of a higher level of ssb than that produced by separate exposures. Hence, lesions are produced by the 254 nm irradiation that are photolyzed through exposure to sunlamp UV greater than 315 nm. Approximately 50% of these lesions are removed following a 2-4 h incubation of the 254-nm-irradiated cells and nearly complete removal is achieved by 16 h. In addition, the profiles for elutions performed at pH 12.8 with cells exposed to the combined treatment were indicative of the presence of alkali labile sites. The repair kinetics of this lesion and alkaline lability of the photolysis product suggest that this photosensitive lesion may represent pyrimidine(6-4)pyrimidone photoproducts. Hence, this approach may represent a relatively simple and sensitive assay for the measurement of this DNA damage.     

Yessotoxin analogues in several strains of Protoceratium reticulatum in Japan determined by liquid chromatography-hybrid triple quadrupole/linear ion trap mass spectrometry

Several strains of Protoceratium reticulatum, one of the dinoflagellates producing yessotoxins (YTXs), were collected from various shellfish producing areas in Japan. YTXs in the cultured strains were analyzed by liquid chromatography-mass spectrometry (LC-MS). Neutral loss scan monitoring, multiple reaction monitoring (MRM) for more than 20 YTX analogues, and full-scan MS/MS spectra obtained with a hybrid triple quadrupole/linear ion trap mass spectrometer showed that yessotoxin (YTX), 45,46,47-trinoryessotoxin (trinorYTX), 1-homoyessotoxin (homoYTX), and 45,46,47-trinor-1-homoyessotoxin (trinor-1-homoYTX) were the dominant toxins in these strains of P. reticulatum. Enone isomer of 42,43,44,45,46,47,55-heptanor-41-oxoyessotoxin (noroxoYTX enone) was also detected in some strains. Toxin profiles and contents were different among the strains. Some strains produced YTX, trinorYTX, 1-homoYTX, trinor-1-homoYTX, and noroxoYTX enone, whereas other strains produced only YTX or 1-homoYTX. This is the first identification of 1-homoYTX and noroxoYTX enone in P. reticulutum in Japan. Some strains did not produce any detectable YTX analogues.     

Rheological, mechanical and transport properties of blown films of high density polyethylene nanocomposites

In this work, high density polyethylene (HDPE) was mixed in a twin screw extruder with organophilic treated clay, Cloisite 20A, and a compatibility agent, a HDPE grafted with maleic anhydride (PEMA). The screw profile was changed from a less dispersive (Profile 1) to a high dispersive configuration (Profile 2). A masterbatch procedure was used to obtain a final organoclay concentration of 5 wt.%. Both profiles allowed the intercalation of the HDPE into the clay, increasing the clay’s gallery distance to 3.7 nm. However, the samples produced with Profile 2 (Nano 2 samples) were more elastic and had a more stable structure than the samples produced with Profile 1. Therefore, two kind of blown films of Nano 2 samples were made: FN1 and FN2. The last one was blown at a higher screw velocity than the FN1. Both films had an increase of 95% in the elastic modulus and a reduction of 60% and 45% in O₂ and water vapor permeability rates, respectively, compared to the film of pure HDPE. However, the FN2 structure was more unstable than the FN1 structure. It was concluded that both screw profiles gave the same level of HDPE intercalation in the clay; however, the more dispersive profile produced more time-stable and elastic structures. The increase in the elongation rate during the film blowing process produced also more time-stable morphologies; however, this higher orientation created matrix/filler interfacial defects.     

Errors in sizing bands of hypervariable DNA profiles on autoradiograms: are they Gaussian?

The accuracy of procedures for sizing hypervariable restriction fragments by Southern blot analysis (SBA) has been tested under three different experimental conditions: (i) intrablot serial analyses: three heterozygous DNA profiles were tested 14 times each in the same gel electrophoresis; (ii) intralaboratory analyses: we replicated three profiles (six autoradiographic bands) in over 100 SBA experiments; (iii) interlaboratory analyses: 15 serial measurements produced in a recent collaborative study (Forensic Sci. Int. 1991, 49, 1-15) were taken into account. In these three cases, a typical U-shaped correlation curve between molecular size and coefficient of variation was found. We explain decrease of accuracy at both extremities of the gels in terms of: (i) enlarged shapes of bands and mean electrophoretic resolution at the cathode; (ii) diffusion and blurring of bands at the anodal edge. The three populations of data were subjected to a chi 2 test and to the Kolmogorov-Smirnov test in order to verify their compliance with normal distribution. Twenty-three out of 27 tests indicated no significant deviation from the assumption of Gaussian distribution. We recommend the adoption of tests for normality to validate the use of symmetric confidence intervals for calculating gene frequencies and asserting a match between adjacent bands.     

In situ time-resolved FTIR spectroelectrochemistry: study of the reduction of TCNQ

The efficiency and versatility of time-resolved FTIR spectroscopy has been used to follow concentration profiles of species produced during a cyclic voltammetric scan. It has been tested in situ and in resolved time, by probing the reduction of tetracyanoquinodimethane (TCNQ) on its first and second electrochemical wave. Besides the establishment of the method, the individual concentrations of TCNQ, of the monoanion and of the dianion were monitored at distinct infrared frequencies and the time derivatives of the concentration profiles were compared to the voltammograms.     

A comparison of theoretically determined and experimentally measured velocity distributions of poly(ethylene terephthalate) flow in a capillary

A streak photographic technique was used to determine the velocity distribution in a capillary produced by the flow of poly(ethylene terephthalate) (PET). This uniquely designed quartz die assembly, which was fitted onto a melt extruder, permitted visualization of polymer flow behavior during melt spinning. Aluminum tracer particles were mixed with polymer chips prior to extrusion. A laser beam was directed through a lens system that illuminated the tracer particles in the melt only in a thin, vertical cross section of the transparent quartz die. A pressure-drop analysis was also performed on PET, under the same experimental conditions, to determine rheological properties of the polymer. By using these rheological properties theoretical velocity distributions were calculated for PET and then compared with the profiles obtained by the streak photographic technique.     

Screening of key odorants and anthocyanin compounds of cv. Okuzgozu (Vitis vinifera L.) red wines with a free run and pressed pomace using GC‐MS‐Olfactometry and LC‐MS‐MS

The principal purpose of the present work is to characterize the aroma, aroma‐active, and anthocyanin profiles of Okuzgozu wines and to observe the effect of the pomace pressing technique on these parameters. A total of 58 and 59 volatile compounds were identified and quantified in free‐run juice wine (FRW) and pressed pomace wine (PW). Alcohols were found as the most dominant group among aroma compounds followed by esters and acids. However, among all these compounds, only 11 and 13 of them could be considered as key odorants in aromatic extracts of FRW and PW, respectively. According to GC‐MS‐O analysis, ethyl octanoate (fruity), phenyl ethyl acetate (fruity), and 2‐phenyl ethanol (flowery) were found as the main contributors to the overall scent of both wines. Beyond the aroma profiles, anthocyanin contents of both types of wines were also investigated, and total 14 and 15 anthocyanins were identified and quantified in FRW and PW. Malvidin‐3‐glycoside and its acetyl and coumaroyl forms were identified as the dominant anthocyanins in both wines. It is worth noting the pressing application (2.0 atm) led to an increase of some unpleasant notes in the aroma providing chemical, pharmacy, and fermented aromas in wine. On the other hand, the wines produced with pressed pomace presented higher amounts of anthocyanins.     

Residue preference mapping of ligand fragments in the Protein Data Bank

The interaction between small molecules and proteins is one of the major concerns for structure-based drug design because the principles of protein-ligand interactions and molecular recognition are not thoroughly understood. Fortunately, the analysis of protein-ligand complexes in the Protein Data Bank (PDB) enables unprecedented possibilities for new insights. Herein, we applied molecule-fragmentation algorithms to split the ligands extracted from PDB crystal structures into small fragments. Subsequently, we have developed a ligand fragment and residue preference mapping (LigFrag-RPM) algorithm to map the profiles of the interactions between these fragments and the 20 proteinogenic amino acid residues. A total of 4032 fragments were generated from 71?798 PDB ligands by a ring cleavage (RC) algorithm. Among these ligand fragments, 315 unique fragments were characterized with the corresponding fragment-residue interaction profiles by counting residues close to these fragments. The interaction profiles revealed that these fragments have specific preferences for certain types of residues. The applications of these interaction profiles were also explored and evaluated in case studies, showing great potential for the study of protein-ligand interactions and drug design. Our studies demonstrated that the fragment-residue interaction profiles generated from the PDB ligand fragments can be used to detect whether these fragments are in their favorable or unfavorable environments. The algorithm for a ligand fragment and residue preference mapping (LigFrag-RPM) developed here also has the potential to guide lead chemistry modifications as well as binding residues predictions.     

A Multivariate Analysis on the Influence of Indigenous Crude Oil Components on the Quality of Produced Water. Comparison Between Bench and Rig Scale Experiments

A matrix of 30 crude oils have been analyzed to investigate if there is any correlation between the physiochemical properties of the crude oils and the quality of the produced water. As an approach to study produced water quality, oil. and brine water (3.5 wt%) have been mixed together, and transmission profiles from the separation process have been investigated by means of Turbiscan LAb. The Turbiscan LAb enables the study of stability of colloidal dispersions without any dilution or modification of the sample. The oil-in-water emulsions (30:70) were made by mixing oil and water at low speed to be sure that they separate within a short period of time. Drop size distributions were investigated for all crude oil emulsions by using a Coulter Counter (COULTER Multisizer II). The correlations between transmission profiles and crude oil characteristics were made by using principal component analysis (PCA), a method that helps visualize the most important information contained in a data set and find combinations of variables that describe major trends. A Vortoil K-liner hydrocyclone connected to a mixing rig has been used to separate oil and water in larger scale experiments. The objective with these experiments was to compare the results with separation experiments done at bench scale. Six crude oils have been investigated at the separation rig, and both droplet size distribution and dispersed oil concentration have been performed. The main conclusions from this work are that Turbiscan LAb is a suitable technique to study the separation of oil-in-water with good reproducibility. The results from the multivariate data analysis show that the crude oils group according to if they are light or heavy and according to if they get high or low transmission. From the larger scale experiments it has been shown that the droplet sizes, oil/water density differential, and viscosity have a significant impact on separation efficiency.     

Direct gas-liquid interfacial dynamics: the reaction between O(3P) and a liquid hydrocarbon

We report the first measurements of internal energy distributions of the OH produced via a direct mechanism, isolated from other components on the basis of time-of-flight, in the interfacial reaction between gas-phase O((3)P) atoms and the liquid hydrocarbon squalane, C(30)H(62). O((3)P) atoms were generated by laser photolysis of NO(2) above the liquid. Resulting hydroxyl radicals that escape from the surface were detected by laser-induced fluorescence. Time-of-flight profiles demonstrate that the kinetic energy of the fastest OH (nu' = 1) is lower than that of (nu' = 0). Rotational distributions were measured at the rising edge of their appearance for both OH (nu' = 0) and (nu' = 1). They were found to differ substantially more than at the peak of their profiles. They were also less dependent on the bulk liquid temperature. We conclude that the new data confirm strongly that at least two mechanisms contribute to the production of OH. The higher-velocity component has translational and rotational energy distributions, observed cleanly for the first time, consistent with a direct mechanism. The close correspondence of these rotational distributions to those from the corresponding homogeneous gas-phase reaction of O((3)P) with smaller hydrocarbons suggests a very similar, near collinear direct abstraction. This is accompanied by a slower component with kinetic energy and rotational (but not vibrational) distributions reflecting the temperature of the liquid, consistent with a distinct trapping-desorption mechanism.     

Gerbils of a seizure-sensitive strain have a mitochondrial inner membrane protein with different isoelectric points from those of a seizure-resistant strain

The distribution of proteins in the cerebral cortex of a seizure-sensitive (SS) strain of gerbil and its seizure-resistant (SR) counterpart was profiled using two-dimensional gel electrophoresis. A series of proteins of similar molecular weight (around 83 kDa) showed small but consistent differences in their isoelectric point (pI) with indistinguishable profiles of distribution between the two strains. Amino acid sequences of peptides produced by limited proteolysis of each protein in the spots from the strains were identical or highly homologous to those of mitofilin, a mitochondrial inner membrane protein (IMMT) in humans. Analysis of cDNA sequences revealed the proteins of these spots to be gerbil mitofilin-like proteins (gIMMT), with a few base substitutions between SS and SR strains, in particular within a region near a putative transmembrane domain that is highly conserved in humans and gerbils. The amino acid at the site was acidic, Glu in humans and Asp in the strain SR of gerbil and a neutral, Asn in strain SS. In addition to these base substitutions, production of multiple species of mRNA for gIMMT by alternative splicing was observed.     

Kinetic isotope effects implicate the iron-oxene as the sole oxidant in P450-catalyzed N-dealkylation

Multiple oxidants have been implicated as playing a role in cytochrome P450-mediated oxidations. Herein, we report results on N-dealkylation, one of the most facile reactions mediated by P450 enzymes. We have employed the N-oxides of a series of para-substituted 13C2H2-labeled N,N-dimethylanilines to function as both substrates and surrogate oxygen atom donors for P450cam and P4502E1. Kinetic isotope effect profiles obtained using the N-oxide system were found to closely match the profiles produced using the complete NAD(P)H/NAD(P)-P450 reductase/O2 system. The results are consistent with oxidation occurring solely through an iron-oxene species.     

Screening Wild Yeast Isolated from Cocoa Bean Fermentation Using Volatile Compounds Profile

Yeasts are one of the main ingredients responsible for flavor precursors production associated with sensorial characteristics in chocolate. Using wild yeast isolated from cocoa beans fermentation is emerging as a strategy for developing starter cultures. However, the volatile compounds (VCs) produced by yeasts are not yet known. This study aimed to select wild yeasts with the potential to produce volatile compounds associated with desirable flavor attributes. A total of 150 wild yeasts strains were isolated from the spontaneous cocoa beans fermentation, of which 40 were identified by morphology and physiological features. VCs produced were identified and quantified using SPME-GC-MS and GC-FID and profiles were evaluated statistically by PCA and cluster analysis for the compounds that had a high odor threshold value. Thirty-six VCs produced by these yeasts were identified into six main families, namely esters, alcohols, acids, aldehydes, ketones, and pyrazines. PCA showed the separation of the yeasts into two main clusters. Strains, Y195 and Y246, belong to the first cluster and are the highest producers of alcohols related to floral perceptions. In the second cluster, thirty-three yeasts were grouped by their ability to produce esters. Of all of them, Y110MRS stood out for producing 2-phenyl ethyl acetate and isoamyl acetate associated with fruity perceptions. This screening allowed us to identify yeasts that produced VCs of technological interest and which could be used to develop a starter culture.