Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Complex Mixtures”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,225 records · Page 68Linked to original sources
PubMed1999

Modulation of genotoxic and related effects by carotenoids and vitamin A in experimental models: mechanistic issues.

The mechanisms involved in the modulation of genotoxic and related effects by carotenoids and vitamin A were inferred from a critical review of an ad hoc constructed database. Almost 500 results were generated in experimental models evaluating the activity of 32 structurally, metabolically and functionally related nutrients, including beta-carotene and 26 other carotenoids, retinol, retinal, all-trans-retinoic acid and retinyl esters. As many as 67 experimental test systems, either in vitro or in vivo, used a variety of cellular targets and/or end-points suggestive of distinctive mechanisms of action. The bulk of available data support the view that carotenoids and vitamin A do not induce genotoxic effects per se. Even in the absence of any genotoxic agent, these nutrients appeared, on the contrary, to display some mechanisms which play protective roles in tumor promotion and progression, such as inhibition of N-myc gene expression resulting in antiproliferative effects, up-regulation of cell-to-cell communication, an increase in connexin 43 gene expression, a decrease in the 'spontaneous' cell transformation frequency and induction of differentiation in vitro. A large number of studies investigated the modulation by carotenoids and vitamin A of genotoxic and related effects produced by 69 genotoxicants, including biological agents, physical agents, chemical compounds and complex mixtures. In spite of some discrepant data, the general trend was that both carotenoids and vitamin A are poorly effective in acting as nucleophiles, nor do they appear to substantially interfere with the induction or repair of DNA damage produced by direct-acting agents. In contrast vitamin A and carotenoids, irrespective of their provitamin A role, in most studies inhibited those genotoxicants which require metabolic activation to electrophilic derivatives in either bacterial or mammalian cells. Coupled with biochemical data, the distinctive patterns observed with genotoxic agents belonging to different chemical classes suggest a complex modulation of both phase I and phase II enzymes involved in the metabolism of xenobiotics. Furthermore, carotenoids and vitamin A shared other protective mechanisms, such as scavenging of genotoxic oxygen species, modulation of signal transduction pathways, inhibition of cell transformation induced by physical and chemical agents, and facilitation of intercellular communication inhibited by genotoxic compounds. Therefore, carotenoids and vitamin A appear to work via multiple mechanisms, which would support a potential protective role in cancer initiation and in the pathogenesis of other mutation-related diseases. These conclusions are consistent with the recognized cancer-preventive activity of these nutrients in certain animal models and with the evidence provided by observational epidemiological studies, which suggested cancer-protective effects at many sites as related to their dietary intake or plasma levels. However, all these lines of evidence and mechanistically based premises contrast with the unexpected outcome of recent clinical intervention trials, which raised the concern that supplemental use of beta-carotene and vitamin A may increase the risk of lung cancer amongst high risk individuals such as tobacco smokers and asbestos-exposed workers.

Animals↗
PubMed2003

Enamel structure properties controlled by engineered proteins in transgenic mice.

UNLABELLED: Amelogenin protein has regulatory effects on enamel biofabrication in mammalian tooth. Using teeth obtained from transgenic mice that express two separate protein-engineered versions of amelogenins, we made structure-nanomechanical properties correlations and showed 21% hardness and 24% elastic modulus degradation compared with the age-matched wildtype littermates. We attribute the inferior properties to the disorganization of the protein matrix resulting in defective mineral formation. INTRODUCTION: Enamel is a bioceramic initiated by the biosynthesis of a complex mixture of proteins that undergoes self-assembly to produce a super molecular ensemble that controls the nucleation and habit of the crystalline mineral phase. Ultimately, the inorganic crystals grow to almost fully replace the organic phase. This biofabrication process occurs at physiologic conditions of pH, temperature, pressure, and ion concentration and results in the hardest tissue in the vertebrate body, with the largest and longest substituted-hydroxyapatite crystals known to biomineralizing systems. The most abundant protein of forming mammalian enamel, amelogenin, has been shown to have a significant regulatory effect on this complex process. MATERIALS AND METHODS: In this work, we present the effect of protein engineering of amelogenin on the mechanical properties of the resultant mouse enamel. We have produced two types of transgenic animals that express separate versions of amelogenin proteins that lack the required self-assembly domains. The resultant matured enamel was extensively characterized for its mechanical properties at the nanoscale by means of nanoindentation and atomic force microscopy (AFM). These techniques have enabled us to probe the mechanical properties that are representative of a single enamel rod. RESULTS: Our nanoindentation measurements have revealed that the altered amelogenin with dysfunctional self-assembly properties resulted in a degradation by as much as 21% in hardness and 24% in elastic modulus compared with the age-matched wildtype littermates. Furthermore, the enamel formed by these defective proteins is found to display a decrease in indentation surface pile-up volume by up to 32%. CONCLUSIONS: We attribute these inferior mechanical properties for the enamel grown by the engineered amelogenins to result from the disorganization of the nanospheres formed in the protein matrix starting at the mineral nucleation stage with a consequential alteration to the fully grown mineral component. By engineering the properties of proteins that contribute to the nanoscale level of hierarchy in enamel biomineralization, it is possible to regulate the properties of the resulting bioceramic at the mesoscale level of the tissue.

Amelogenin↗
PubMed2003

Chemical cross-linking and mass spectrometry for mapping three-dimensional structures of proteins and protein complexes.

Chemical cross-linking of proteins, an established method in protein chemistry, has gained renewed interest in combination with mass spectrometric analysis of the reaction products for elucidating low-resolution three-dimensional protein structures and interacting sequences in protein complexes. The identification of the large number of cross-linking sites from the complex mixtures generated by chemical cross-linking, however, remains a challenging task. This review describes the most popular cross-linking reagents for protein structure analysis and gives an overview of the strategies employing intra- or intermolecular chemical cross-linking and mass spectrometry. The various approaches described in the literature to facilitate detection of cross-linking products and also computer software for data analysis are reviewed. Cross-linking techniques combined with mass spectrometry and bioinformatic methods have the potential to provide the basis for an efficient structural characterization of proteins and protein complexes.

Binding Sites↗
PubMed1991

NADH:ubiquinone oxidoreductase from bovine heart mitochondria. cDNA sequences of the import precursors of the nuclear-encoded 39 kDa and 42 kDa subunits.

The 39 kDa and 42 kDa subunits of NADH:ubiquinone oxidoreductase from bovine heart mitochondria are nuclear-coded components of the hydrophobic protein fraction of the enzyme. Their amino acid sequences have been deduced from the sequences of overlapping cDNA clones. These clones were amplified from total bovine heart cDNA by means of the polymerase chain reaction, with the use of complex mixtures of oligonucleotide primers based upon fragments of protein sequence determined at the N-terminals of the proteins and at internal sites. The protein sequences of the 39 kDa and 42 kDa subunits are 345 and 320 amino acid residues long respectively, and their calculated molecular masses are 39,115 Da and 36,693 Da. Both proteins are predominantly hydrophilic, but each contains one or two hydrophobic segments that could possibly be folded into transmembrane alpha-helices. The bovine 39 kDa protein sequence is related to that of a 40 kDa subunit from complex I from Neurospora crassa mitochondria; otherwise, it is not related significantly to any known sequence, including redox proteins and two polypeptides involved in import of proteins into mitochondria, known as the mitochondrial processing peptidase and the processing-enhancing protein. Therefore the functions of the 39 kDa and 42 kDa subunits of complex I are unknown. The mitochondrial gene product, ND4, a hydrophobic component of complex I with an apparent molecular mass of about 39 kDa, has been identified in preparations of the enzyme. This subunit stains faintly with Coomassie Blue dye, and in many gel systems it is not resolved from the nuclearcoded 36 kDa subunit.

Amino Acid Sequence↗
PubMed2003

Effects of postnatal exposure to mixtures of non-ortho-PCBs, PCDDs, and PCDFs in prepubertal female rats.

There are concerns that postnatal exposure to organochlorines present in breast milk could lead to adverse health effects. We reconstituted four mixtures of aryl-hydrocarbon receptor (AhR) agonists (3 non-ortho polychlorinated biphenyls [PCBs], 6 polychlorinated dibenzodioxins [PCDDs], 7 polychlorinated dibenzofurans [PCDFs], or all 16 chemicals together [referred to as AhRM]) based on their concentrations in breast milk, and examined their effects following exposure by gavage from day 1 until day 20 of age. Female neonates received dosages of AhRM equivalent to 1, 10, 100, or 1000 times the amount consumed by an infant over the first 24 days of life. Other groups received the PCBs, the PCDDs, or the PCDFs at the 1000x level. All rats were sacrificed at 21 days of age. Changes in ethoxyresorufin-o-deethylase hepatic activity, thymus and body weights, and serum thyroxin were linked to the 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) toxic equivalents (TEQ) of the four mixtures (1000x-AhRM > PCDDs > PCBs > PCDFs). To test for AhRM antiestrogenicity, two additional groups received 1.5 microg/kg of 17alpha-ethynyl estradiol (EE) with or without the 1000x-AhRM. The AhRM had no effect on uterine weight or EE-stimulated uterine growth. The actions of the combined EE and AhRM treatments suggest additive effects in decreasing pentoxyresorufin-o-deethylase activity and spleen weight, but nonadditive/antagonistic effects on adrenal weight and serum thyroxin. In conclusion, (1) 10x-AhRM had no detectable effects, (2) TEQ values relate to observed toxicities, even when testing complex mixtures of AhR agonists, and (3) indications of tissue-specific additive and nonadditive/antagonistic effects, but no synergism, were observed when doses of AhRM were increased, or combined with EE.

Animals↗
PubMed1988

Detection and microsequencing of juvenile hormone-binding proteins of an insect by the use of an iodinated juvenile hormone analog.

An [125I]iodinated juvenile hormone (JH) analog can be used as a sensitive and highly selective probe for the visualization of high-affinity, (JH)-specific binding proteins from insect hemolymph samples. The proteins can be detected in their native form using a two-dimensional (isoelectric focusing then native gradipore gel) separation of the crude protein mixture containing the 125I-labeled iodinated JH analog. The proteins can be transferred to activated glass fiber paper by electroblotting, and the location of the bound gamma-emitter can be found by exposure of the dried gel or the electroblot to X-ray film. The radiolabeled protein spot can be excised from the Coomassie-stained glass fiber paper and subjected directly to gas-phase N-terminal amino acid sequencing. This non-destructive, non-denaturing technique may have wide applicability in identifying and sequencing ligand-specific binding proteins in complex mixtures.

Amino Acid Sequence↗
PubMed2003

Solid-phase extraction NMR studies of chromatographic fractions of saponins from Quillaja saponaria.

The saponin mixture QH-B from the tree Quillaja saponaria var. Molina was fractionated by RP-HPLC in several steps. The fractions were analyzed by solid-phase extraction NMR (SPE-NMR), a technique combining the workup by solid-phase extraction with on-line coupling to an NMR flow probe. Together with MALDI-TOF mass spectrometry and comparison with chemical shifts of similar saponins, the structures of both major and minor components in QH-B could be obtained. The procedure described is a simple method to determine the structure of components in a complex mixture. The two major fractions of the mixture were found to contain at least 28 saponins, differing in the carbohydrate substructures. Eight of these have not previously been determined. The 28 saponins formed 14 equilibrium pairs by the migration of an O-acyl group between two adjacent positions on a fucosyl residue.

Adjuvants, Immunologic↗
PubMed1998

Peroxynitrite increases the degradation of aconitase and other cellular proteins by proteasome.

We report that exposure of aconitase to moderate concentrations of peroxynitrite, 3-morpholinosydnonimine (SIN-1; a superoxide- and nitric oxide-liberating substance), or hydrogen peroxide, inhibits the enzyme and enhances susceptibility to proteolytic digestion by the isolated 20 S proteasome. Exposure to more severe levels of oxidative stress, from these same agents, causes further inhibition of the enzymatic activity of aconitase but actually decreases its proteolytic breakdown by proteasome. It should be noted that the superoxide and nitric oxide liberated by SIN-1 decomposition react to form a steady flux of peroxynitrite. S-Nitroso-N-acetylpenicillamine, a compound that liberates nitric oxide alone, causes only a small loss of aconitase activity (25% or less) and has no effect on the proteolytic susceptibility of the enzyme. Proteasome also seems to be the main protease in cell lysates that can degrade aconitase after it has been oxidatively modified by exposure to peroxynitrite, SIN-1, or hydrogen peroxide. Using cell lysates isolated from K562 cells treated for several days with an antisense oligodeoxynucleotide to the initiation codon region of the C2 subunit of proteasome (a treatment which diminishes proteasome activity by 50-60%), the enhanced degradation of moderately damaged aconitase was essentially abolished. Other model proteins as well as complex mixtures of proteins, such as cell lysates, also exhibit enhanced proteolytic susceptibility after moderate SIN-1 treatment. Therefore we conclude that peroxynitrite reacts readily with proteins and that mild modification by peroxynitrite results in selective recognition and degradation by proteasome.

Aconitate Hydratase↗
PubMed2005

Capillary electrophoresis separation of a mixture of chitin and chitosan oligosaccharides derivatized using a modified fluorophore conjugation procedure.

A capillary electrophoresis (CE) method was developed for the simultaneous analysis of small chitin and chitosan oligosaccharides. For detection purposes, the oligomers were derivatized with 8-aminopyrene-1,3,6-trisulfonic acid (APTS), a well known fluorophore for oligosaccharides analysis. The detection was performed by laser-induced fluorescence (LIF) with an argon ion laser having an excitation wavelength of 488 nm and with emission monitored at 520 nm. Derivatization parameters such as reaction time and conditions were examined. Separation conditions were also varied by testing a range of buffer pHs and concentrations. The best conditions were found using an 80 mM borate buffer at pH 8.4. This CE-LIF optimized method was used for the analysis of an enzymatically produced oligo-chitosan sample composed of a complex mixture and having an average degree of polymerization of 3.7 monomer units and 80% deacetylation. The oligo-chitosan sample was treated with a chitin deacetylase-like enzyme, the products were derivatized with APTS, and then analyzed without purification. The goal was to determine whether the deacetylase-like enzyme could increase the extent of deacetylation of the oligo-chitosan sample.

Amidohydrolases↗
PubMed2006

Pre-exposure to a novel nutritional mixture containing a series of phytochemicals prevents acetaminophen-induced programmed and unprogrammed cell deaths by enhancing BCL-XL expression and minimizing oxidative stress in the liver.

From a disease-prevention perspective, recent progress in phytochemical and nutraceutical research clearly suggests (benefits outweigh the risk pattern). Although powerful antioxidant properties have been the most acclaimed mechanism of action for these entities, the individual antioxidants studied in clinical trials do not appear to have consistent preventative effects. The actions of the antioxidant nutrients alone do not explain the observed health benefits of diets rich in fruits and vegetables for chronic diseases. Therefore, we proposed that the additive and synergistic effects of phytochemicals in fruits and vegetables are responsible for these potent antioxidant and anticancer activities, and that the benefit of a diet rich in fruits and vegetables is attributed to the complex mixture of phytochemicals present in plants [1]. Surprisingly, however, no studies have attempted to evaluate the combined antitoxic potential of a phytochemical-nutraceutical mixture (PNM) in in vivo models. Therefore, this study, for the first time, was designed to investigate whether pre-exposure to a unique PNM has the ability to impede mechanistic events involved in acetaminophen (APAP)-induced hepatotoxicity. Besides several vitamins and minerals in balanced proportions (approximately US RDA), the PNM used in this investigation contained several well-known phytochemicals such as citrus flavonoids, red wine polyphenols, Garcinia, Gymnema, Ginkgo, Ephedra sinica, Camellia sinensis, Silybum, Guarana, Eluthero, Allium sativum and Ocimum basilicum extracts. To evaluate PNM's antitoxic potential, groups of animals ICR mice, 3 months old) received either a control diet or PNM containing diets (1X and 10X) for 4 weeks. On day-28, animals were divided into two subgroups. Half the animals were administered normal saline and the other half received 400mg/kg ip injections of APAP. All the animals were sacrificed 24h after APAP exposure. Serum and tissue (liver and kidneys) samples were analyzed. APAP alone caused massive liver injury (nearly 495-fold increase in ALT) and oxidative stress (Lipid peroxidation: 268% increase in MDA) coupled with genomic DNA fragmentation (288% increase). Exposure to 1X-PNM for 28 days significantly reduced animal mortality and all the APAP-induced biochemical events (In 1X-PNM + AP: ALT leakage decreased to 54 fold; MDA accumulation decreased to 125%, and DNA fragmentation decreased to 122%), whereas 10X-PNM + APAP slightly escalated both oxidative stress and genomic DNA fragmentation preceding liver injury. Liver homogenates subjected to western blot analysis disclosed the ability of 1X-PNM to counteract APAP-induced decrease in Bcl-xL expression. Histopathological evaluation of stained liver tissue sections indicated anti-apoptogenic and anti-necrogenic reponses coupled with near complete prevention of glycogen depletion by 1X-PNM. Collectively, our investigation suggests that a mixture containing an assortment of phytochemicals/nutraceuticals may serve as a much more powerful blend in preventing drug or chemical-induced organ injuries than a single phytochemical or nutraceutical entity. In addition, ephedra and caffeine containing PNM-exposure in a controlled manner may potentially shield vital target organs from toxicities caused by intentional, unintentional or accidental exposures to structurally and functionally diverse drug and chemical entities.

Acetaminophen↗
PubMed1995

Structure of a novel oligosaccharide-mycosporine-amino acid ultraviolet A/B sunscreen pigment from the terrestrial cyanobacterium Nostoc commune.

Water-soluble UV-A/B-absorbing pigments are secreted by cells of the cosmopolitan terrestrial cyanobacterium Nostoc commune. The pigments constitute a complex mixture of monomers with molecular masses of up to 1801 Da. Two different chromophores with absorption maxima at 312 and 335 nm are linked to different amino acids and to oligosaccharides consisting of galactose, glucose, xylose, glucuronic acid, and glucosamine. The 335 nm chromophore is a 1,3-diaminocyclohexen derivative, while the chromophore with an absorption maximum at 312 nm is most likely a 3-aminocyclohexen-1-one derivative. These UV-inducible substances are the first mycosporines to be described covalently linked to oligosaccharides. The pigments are located in the extracellular glycan sheath of Nostoc colonies, where they form complexes of extremely high molecular mass that are attached noncovalently to the glycan sheath. Pigments occur in concentrations that permit the cells to attenuate a significant part of incident UV-B radiation.

Amino Acids↗
PubMed2006

Contribution of host lipids to Toxoplasma pathogenesis.

As an actively dividing organism, the intracellular parasite Toxoplasma gondii must adjust the size and composition of its membranes in order to accommodate changes due to housekeeping activities, to commit division and in fine to produce new viable progenies. Lipid inventory of T. gondii reveals that the biological membranes of this parasite are composed of a complex mixture of neutral and polar lipids. After examination of the origin of T. gondii membrane lipids, three categories of lipids can be described: (i) lipids scavenged by T. gondii from the host cell; (ii) lipids synthesized in large amounts by the parasite, independently from its host cell; and (iii) lipids produced de novo by the parasite, but whose synthesis does not come close to satisfying the entire parasite's needs. These latter must be adeptly acquired from the host environment. To this end, T. gondii diverts a large variety of lipid precursors from host cytoplasm and efficiently manufacture them into complex lipids. This rather remarkable reliance on host lipid resources for parasite survival opens new avenues to restrict parasite growth. Indeed, parasite starvation can be induced upon deprivation from essential host lipids. Lipid analogues with anti-proliferative properties are voraciously taken up by the parasites, which results in parasite membrane defects, and ultimately death.

Animals↗
PubMed2003

Reduction of chemical formulas from the isotopic peak distributions of high-resolution mass spectra.

A method has been developed for the reduction of the chemical formulas of compounds in complex mixtures from the isotopic peak distributions of high-resolution mass spectra. The method is based on the principle that the observed isotopic peak distribution of a mixture of compounds is a linear combination of the isotopic peak distributions of the individual compounds in the mixture. All possible chemical formulas that meet specific criteria (e.g., type and number of atoms in structure, limits of unsaturation, etc.) are enumerated, and theoretical isotopic peak distributions are generated for each formula. The relative amount of each formula is obtained from the accurately measured isotopic peak distribution and the calculated isotopic peak distributions of all candidate formulas. The formulas of compounds in simple spectra, where peak components are fully resolved, are rapidly determined by direct comparison of the calculated and experimental isotopic peak distributions. The singular value decomposition linear algebra method is used to determine the contributions of compounds in complex spectra containing unresolved peak components. The principles of the approach and typical application examples are presented. The method is most useful for the characterization of complex spectra containing partially resolved peaks and structures with multiisotopic elements.

Journal Article↗
PubMed1996

High-precision D/H measurement from organic mixtures by gas chromatography continuous-flow isotope ratio mass spectrometry using a palladium filter.

Continuous-flow high-precision determination of D/H ratios from an organic mixture is described using gas chromatography coupled to a Pd filter system as an interface for isotope ratio mass spectrometry. A gas chromatograph and combustion and reduction furnaces are connected to a Pd filter via a postcolumn head pressure makeup gas to increase chromatographic sensitivity. This interface is evaluated using benzene as an internal standard in a mixture of ethylbenzene and cyclohexanone in hexane with analyte quantities of < 3 ng (< 300 pg of H). A calibration curve is constructed using four benzene samples over a range of -48 to 372/1000 (delta DSMOW), resulting in an average benzene D/H precision of SD < 5/1000 (delta DSMOW) and deviations of < 4/1000 from the calibration curve. Ethylbenzene and cyclohexanone of a single D enrichment are analyzed as unknowns in three sample mixtures with varying D-enriched benzene and result in precisions of SD < 5/1000. No apparent memory is observed between peaks of differently enriched analytes within the same chromatogram. All results are corrected for ion source nonlinearities characteristic of hydrogen analysis, using the internal peakwise correction algorithm, described previously. A small dependence of isotope ratio on palladium membrane temperature is demonstrated over a range of 4 degrees C; therefore, with tighter control of palladium temperature, precision can probably be improved. The data indicate that this system is useful for rapid continuous-flow IRMS analysis of D/H ratios from organics in complex mixtures characteristic of geological and biological samples.

Benzene Derivatives↗
PubMedDate not supplied

Conjugated linoleic acids: all the same or to everyone its own function?

Conjugated linoleic acid (CLA) is a generic term referring to a mixture of geometrical and positional isomers of linoleic acid in which up to 16 members have been identified. Many potentially beneficial health effects have been ascribed to these fatty acids when consumed as a mixture, and where generally 2 isomers dominate, e.g. the 9c, 11t-isomer, the so-called rumenic acid, and the 10t, 12c-isomer: anti-carcinogenic, immune modulator, anti-atherosclerotic, and anti-obesity among the most spectacular. The question arises as to whether the pleiotropic biological activity is supported by one or several of the isomers. Recent studies using pure individual isomers have started to elucidate this issue, but many others are required to ascribe a respective role to each CLA isomer (the main ones as well as the minor ones), such as those occurring in some complex mixtures already commercially available, or even in foodstuff. The aim of the present study was to focus on the CLA-isomer specific effects depicted in the literature up to now.

Animals↗
PubMed1999

Investigation of combwax of honeybees with high-temperature gas chromatography and high-temperature gas chromatography-chemical ionization mass spectrometry. I. High-temperature gas chromatography.

The combwaxes of the honeybee species Apis mellifera, Apis cerana, Apis dorsata, Apis laboriosa, Apis florea and Apis andreniformis have been examined by high-temperature gas chromatography. Combwax consists of a complex mixture of homologous neutral lipids. These compounds containing up to 64 carbons were chromatographed intact on a 10 m x 0.2 mm high-temperature stable SOP-50-PFD (50%-diphenyl/50%-1H,1H,2H,2H-perfluorodecylmethylpolysiloxane)-co ated Duran glass capillary column. The use of this stationary phase results in lower retention values and, at last, in lower thermal stress of the analytes. In order to minimize the discrimination effect due to adsorption and/or degradation, a two-step derivatization was performed resulting in the formation of tert.-butyldimethylsilyl esters of the long chain fatty acids and trimethylsilyl ethers of complex hydroxyesters, respectively. The derivatization procedure was optimized using a modification of the extended Donike test. In addition this test allows the quantification of the thermal stability of the derivatives performed. The derivatization procedure was applied for combwax analysis. More than 80 compounds were separated and their peak areas semiquantitatively exploited.

Animals↗
PubMed1994

Intraepithelial lymphocytes and their recognition of non-classical MHC molecules.

Recent studies of the TCR alpha and beta chains expressed by normal human IELs suggest that these intestinal lymphocytes are directed at a limited set of antigens, presumably on intestinal epithelial cells in view of their anatomic location. The direct sequence analysis of these cells has indicated that they are oligoclonal and cannot, therefore, be responding to the complex mixture of antigens which are present in the lumen. The abundant expression of the CD8 accessory molecule by the IELs, in addition, indicates that these putative intestinal epithelial cell antigens are presented by MHC class I or I-like molecules. The expression of CD8 also suggests that these cells function biologically in part as cytolytic T lymphocytes which is consistent with a variety of functional studies. Taken together with their expression of the CD45RO isoform, these phenotypic and functional observations suggest that iIELs are cytolytic, memory cells which are responsive to an extremely limited number of antigens bound to major histocompatibility complex (MHC) class I or class I-like molecules. Several non-polymorphic MHC class I-like molecules such as Qa, the thymus leukemia antigen (TL) and CD1 in the mouse and CD1 in human represent important candidate ligands for these oligoclonal iIELs. TL and CD1 are expressed specifically by murine intestinal epithelial cells. In humans, CD1d is constitutively expressed by intestinal epithelial cells. In addition, we have isolated iIEL T cell clones which specifically recognize members of the CD1 gene family when expressed on a transfected B cell line that lacks HLA-A and B and have shown that the proliferation of peripheral blood T cells to intestinal epithelial cells is CD1d dependent. Thus, the evidence to date strongly implicate the nonpolymorphic, class Ib molecules as novel restriction elements for unique populations of lymphocytes within the intestinal epithelium.

Animals↗
PubMed2006

ChromAlign: A two-step algorithmic procedure for time alignment of three-dimensional LC-MS chromatographic surfaces.

We present an algorithmic approach to align three-dimensional chromatographic surfaces of LC-MS data of complex mixture samples. The approach consists of two steps. In the first step, we prealign chromatographic profiles: two-dimensional projections of chromatographic surfaces. This is accomplished by correlation analysis using fast Fourier transforms. In this step, a temporal offset that maximizes the overlap and dot product between two chromatographic profiles is determined. In the second step, the algorithm generates correlation matrix elements between full mass scans of the reference and sample chromatographic surfaces. The temporal offset from the first step indicates a range of the mass scans that are possibly correlated, then the correlation matrix is calculated only for these mass scans. The correlation matrix carries information on highly correlated scans, but it does not itself determine the scan or time alignment. Alignment is determined as a path in the correlation matrix that maximizes the sum of the correlation matrix elements. The computational complexity of the optimal path generation problem is reduced by the use of dynamic programming. The program produces time-aligned surfaces. The use of the temporal offset from the first step in the second step reduces the computation time for generating the correlation matrix and speeds up the process. The algorithm has been implemented in a program, ChromAlign, developed in C++ language for the .NET2 environment in WINDOWS XP. In this work, we demonstrate the applications of ChromAlign to alignment of LC-MS surfaces of several datasets: a mixture of known proteins, samples from digests of surface proteins of T-cells, and samples prepared from digests of cerebrospinal fluid. ChromAlign accurately aligns the LC-MS surfaces we studied. In these examples, we discuss various aspects of the alignment by ChromAlign, such as constant time axis shifts and warping of chromatographic surfaces.

Algorithms↗