Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Matrix Bands”

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 811 records · Page 45Linked to original sources
PubMed2006

Ring opening of 2,5-didehydrothiophene: matrix photochemistry of C4H2S isomers.

Irradiation (lambda > 254 nm) of matrix-isolated 2,5-diiodothiophene (10) gives rise to IR bands assigned to ethynylthioketene (6). Diethynyl sulfide (3), which would form in the process of retro-Bergman cyclization of the incipient 2,5-didehydrothiophene (4), is not detected. Under the same irradiation conditions, matrix-isolated diethynyl sulfide (3) rearranges to thioketene 6 and butatrienethione (5), the global minimum on C4H2S potential energy surface. The photochemical formation of thioketene 6 from either diyl 4 or sulfide 3 may be interpreted in line with a recent computational prediction on the thermal ring opening of diyl 4, which favors C-S bond cleavage, leading to 6, over C-C bond cleavage, leading to 3. Photolysis of matrix-isolated 3,4-thiophenedicarboxylic acid anhydride (11) enables the observation of the photoequilibration of three low-energy C4H2S isomers, butatrienethione (5), ethynylthioketene (6), and butadiynylthiol (7), via apparent [1,3]-hydrogen shifts.

Journal Article↗
PubMed1996

Phylogenetic history of LINE-1 among arvicolid rodents.

The extent of restriction fragment sharing among arvicolid rodents was examined following Southern blotting with a reverse transcriptase region probe from long interspersed nuclear element 1 (LINE-1 or L1). DNAs from 30 species belonging to nine genera were digested with 11 restriction endonucleases. Following hybridization discrete bands were scored with respect to their presence or absence and intensity, and both within- and between-species comparisons were conducted. Intraspecific analyses revealed low but detectable levels of variation. Interspecific comparisons revealed three groups of bands: those present in all 30 species (6 out of a total of 248 bands), those phylogenetically informative in two or more species (130 out of 248), and those unique to a single species (114 out of 248). A multistate data matrix consisting of species by codes representing the intensities of informative bands was analyzed by maximum parsimony. Further, distance values between species were converted to rates using estimated fossil divergence times. Both the parsimony and rate analyses revealed differences between species in the extent of band sharing and in the intensities of common bands, indicating that the amplification and movement of LINE elements has occurred in episodic bursts during the history of this group. Systematic interpretations of the evolutionary trees were concordant with those previously obtained using other data sets, suggesting that although the amplification of repetitive sequences may occur episodically in this taxonomic group, there do appear to be some constraints.

Animals↗
PubMed2006

In vitro culture conditions favoring selection of chromosomal abnormalities in human ES cells.

Previous studies in several laboratories have demonstrated inadvertent chromosomal abnormalities in long-term cultured human embryonic stem cells (HESC). Here, using a two-step selection process we report a functional adaptation of a HESC line, HS181, towards a decreased dependence of extra cellular matrix (ECM) for in vitro survival, that is for growth directly onto a plastic surface. Successful adaptation was paralleled with a karyotype change in 100% of the cells to 47,XX,del(7)(q11.2),+i(12)(p10). The resulting adapted population showed increased survival and growth on plastic and also maintained expression of HESC markers, but showed a decreased pluripotency, as demonstrated by results from embryoid body (EB) formation in vitro. The finding of reduced pluripotency may not be totally unexpected since the variant cells were selected for self-renewal and proliferation, not differentiation during the adaptation to growth on plastic. In the light of recent models of a germ cell origin of HESC it is of particular interest that similar to many of the reported spontaneous HESC mutants, one of the identified specific chromosome abnormalities, i(12p), has also been strongly implicated for human germ cell cancer. However, the mutated HESC variant carrying this mutation failed to grow as a xeno-graft in a mouse model in vivo. This is surprising and needs a further mechanistic analysis for its explanation. Increased knowledge of genetic integrity of HESC may have significance on the understanding of mechanisms for tumor progression and thus strategy for treatments, particularly for tumors occurring in early life.

Animals↗
PubMed1988

Short and long ultradian EEG components in daytime arousal.

In order to investigate the spatio-temporal organization of the daytime arousal state, polygraphic recordings were obtained on 9 subjects, during the period from 11.00 a.m. to 19.30 p.m. Multiple sleep latency tests (MSLTs) administered every 20 min were used as an objective index of sleepiness. Long-duration, wide-band EEG was analyzed by principal components analysis (PCA) to extract the features of ultradian rhythmicities. The data matrix for PCA was constructed from the percentage-power values of 16 frequency bands (2-18 Hz). The diurnal rhythm of the arousal EEG was made up of 2 ultradian components with periods of about 100 min and 3-8 h. The shorter component is thought to represent the oscillation of vigilance level between mental 'rest' and 'activity' states in the basic rest-activity cycle (BRAC). The longer component is thought to represent variations in levels of consciousness between 'wakefulness' and 'drowsiness' states. Our interpretation of the data suggests that the shorter component is superimposed upon the longer one, and that the specific arousal state involved in the shorter ultradian rhythmicity changes to another state at around the 'breaking point' in mid-afternoon.

Activity Cycles↗
PubMed2005

Trifluoromethanesulfenyl acetate, CF3S-OC(O)CH3, and trifluoromethanesulfenyl trifluoroacetate, CF3S-OC(O)CF3: unexpected conformational properties.

Structural and conformational properties of two sulfenyl derivatives, trifluoromethanesulfenyl acetate, CF3S-OC(O)CH3 (1), and trifluoromethanesulfenyl trifluoroacetate, CF3S-OC(O)CF3 (2), were determined by gas electron diffraction, vibrational spectroscopy, in particular with IR (matrix) spectroscopy, which includes photochemical studies, and by quantum chemical calculations. Both compounds exist in the gas phase as a mixture of two conformers, with the prevailing component possessing a gauche structure around the S-O bond. The minor form, 15(5)% in 1 and 11(5)% in 2 according to IR(matrix) spectra, possesses an unexpected trans structure around the S-O bond. The C=O bond of the acetyl group is oriented syn with respect to the S-O bond in both conformers. UV-visible broad band irradiation of 1 and 2 isolated in inert gas matrixes causes various changes to occur. Conformational randomization clearly takes place in 2 with simultaneous formation of CF3SCF3. For 1 the only reaction channel detected leads to the formation of CH3SCF3 with the consequent extrusion of CO2. Quantum chemical calculations (B3LYP/6-31G and MP2 with 6-31G and 6-311G(2df,pd) basis sets) confirm the existence of a stable trans conformer. The calculations reproduce the conformational properties for both compounds qualitatively correct with the exception of the B3LYP method for compound 2 which predicts the trans form to be prevailing, in contrast to the experiment.

Journal Article↗
PubMed1988

Laboratory studies of the infrared spectral properties of CO in astrophysical ices.

Analysis of laboratory spectra of numerous astrophysical ice analogs demonstrates that the exact band position, width, and profile of the solid state CO fundamental near 2137 cm-1 (4.679 microns) can provide important information on the physical conditions present during the ice accretion phase as well as during any subsequent thermal processes and radiation exposure. In the ices studied, the CO peak position varies from 2134 to 2144 cm-1 (4.686 to 4.664 microns) and the band width from 2.1 to over 20 cm-1 depending on the composition of the ice. In an ice matrix dominated by H2O, the CO peak falls at 2136.7 cm-1, has a full width at half-maximum of about 9 cm-1, and shows a prominent sideband at 2152 cm-1. This sideband and minor structure superposed on the main band arise from CO trapped in different matrix sites. These features provide information concerning the thermal and radiation history of the ice. The solid CO band in interstellar spectra often has contributions from broad (12 cm-1) and narrow (5 cm-1) components. We identify the broad component with CO intimately mixed in matrices dominated by polar molecules, of which H2O is likely to be the major component. Examination of the interstellar and laboratory band profiles shows that either the abundance of nonpoplar impurities in these ices must be less than 10% or the ices have been thermally annealed or processed by ultraviolet radiation. The narrow component is likely to originate from grain mantles dominated by nonpolar molecules such as CO2. These components reflect differences in the physical and chemical conditions in regions of the cloud along the line of sight. Laboratory determination of the absorption strength of the CO fundamental in H2O-rich ices showed that the value used in the past was approximately 60% too low and that most previously determined solid-state CO column densities have been systematically overestimated. The rich spectral behavior of the CO band observed in the laboratory studies clearly indicates that future high-quality astronomical spectra in the 2200-2100 cm-1 range can produce a wealth of new information and provide deeper insights into the nature of astrophysical ices.

Astronomical Phenomena↗
PubMed1978

Electron microscopy of peroxidase and acid phosphatase in leprous and uninfected armadillo macrophages: a macrophage subpopulation contains peroxisomes and lacks bacilli.

Lepromatous tissue from armadillos inoculated 24--36 months earlier with Mycobacterium leprae was obtained for electron microscopic studies. Cytochemically stained lepromas revealed a subpopulation of macrophages containing peroxisomes. These peroxidase reactive macrophages were not infected with bacilli. Acid phosphatase was present in macrophages and many of these were infected with bacilli and contained vacuoles and lipid globules. Within the membrane-bound vacuoles, acid phosphatase surrounded bacilli. However, the reaction product ended abruptly at a 15--40 millimicron thick zone of low electron density surrounding intact bacilli. Acid phosphatase was more intensely reactive and localized less precisely in heavily infected and vacuolated macrophages than in lightly and non-infected cells. The effectiveness of this bacillary barrier and the numerous infected macrophages with substantial acid phosphatase argue against the ability of acid phosphatase to protect host cells from leprosy bacilli. Evidence suggests a protective action of peroxidase or the rapid turnover of macrophages within lepromas. Granular and membranous debris were commonly seen within vacuoles of infected macrophages. A portion of the debris was ultrastructurally similar to bacillary matrix and was nonreactive for peroxidase and acid phosphatase. Following homogenization and centrifugation, similar materials banded with bacilli above 60% sucrose. Another portion of the debris was ultrastructurally similar to host lysosomal matrix and was reactive for acid phosphatase. Results support the concept of dual host and parasitic origins of the debris found in phagolysosomes of infected macrophages. Transparent, oval Epon defects remained eccentric to the majority of intact bacilli in centrifuged fractions. Apparently, an intrinsic property of leprosy produced these Epon defects.

Acid Phosphatase↗
PubMed1982

In vitro histological and tetracycline staining properties of surface layer rat incisor enamel also reflect the cyclical nature of the maturation process.

Rat incisors cleaned of overlying enamel organ cells stain unevenly with several common histological stains producing two kinds of banding pattern. In one a pattern of widely spaced stained bands run in an oblique to transverse direction from a more apical level on the medial side to a more incisal level on the lateral side of each tooth. The pattern correlated directly with that produced by both in vivo and in vitro short-term tetracycline labelling in the same teeth: it also resembled the patterns previously demonstrated in a) horseradish peroxidase penetration into lateral intercellular spaces between maturation ameloblasts, b) the distribution of enamel labelling in vivo with 45Ca, c) of etching of enamel surfaces demineralized with EDTA with the glutaraldehyde fixed enamel organ in situ and d) in the distribution of smooth-ended and ruffled border types of cell specializations. We conclude that these bands demonstrate further and previously unrecognised aspects of the cyclical phenomena in enamel maturation-mineralization and show cyclical differences in the physico-chemical status of the organic matrix in the maturation process. A second, incremental growth type of banding pattern occurred at 200-225 micron intervals in the lower incisors and had the same distribution at the beginning and end of the maturation zone.

Animals↗
PubMed2004

Mechanism of adhesion and detachment at the anterior end of Merizocotyle icopae (Monogenea: Monocotylidae) including ultrastructure of the anterior adhesive matrix.

The anterior adhesive mechanism was studied for Merizocotyle icopae (Monogenea: Monocotylidae). Adult anterior apertures can open and close. In addition, duct endings terminating within the apertures are everted or retracted depending on the stage of attachment. Adhesive in adults is synthesized from all 3 secretory types (rod-shaped, small and large spheroidal bodies) found within anterior apertures. All exit together and undergo mixing to produce the adhesive matrix, a process that depletes duct contents. A greater number of ducts carrying rod-shaped bodies is depleted than ducts containing spheroidal bodies which changes the ratio of secretory types present on detachment. Detachment involves elongation of duct endings and secretion of additional matrix as the worm pulls away from the substrate. The change in secretory type ratio putatively modifies the properties of the secreted matrix enabling detachment. Only after detachment do ducts refill. During attachment, individual secretory bodies undergo morphological changes. The larval and adult adhesive matrix differs. Anterior adhesive in oncomiracidia does not show fibres with banding whereas banded fibres comprise a large part of adult adhesive. The data suggest that this is the result of adult spheroidal secretions modifying the way in which the adult adhesive matrix forms.

Adhesiveness↗
PubMed1996

Synthetic scleral reinforcement materials. II. Collagen types in the fibrous capsule.

Attainment of a steady state in fibrous-capsule formation around a polymeric implant is indicative of minimization of the foreign-body response, and is characterized by thin capsule walls, few macrophages, and the replacement of type III collagen with type I collagen within the capsular matrix. We implanted four general types of extraocular band materials (porous, solid, composite, and patched) in rabbit eyes, and examined the proportions of types III and I collagen in the surrounding fibrous-capsule walls at intervals after surgery. Immunohistochemical analysis showed that 18 months after implantation of the band materials, the capsules adjacent to the porous-material surfaces had virtually no type III collagen remaining, while the solid-surface-material capsules still contained more than trace amounts (greater than 5%). In that the bands were implanted around the outside of the globe, which provides a dynamic environment in constant motion, it may be that the cellular ingrowth permitted by the porous materials increased the stability of the implants, thereby lessening the foreign body response and allowing the collagen replacement characteristic of the steady state to be completed. In contrast the solid-surface implants, which had little cellular ingrowth, may have continued to undergo sufficient micromovement within the capsule walls to sustain a low-level activation of the wound-healing response, resulting in thicker capsule walls and residual type III collagen a year and a half after implantation surgery.

Animals↗
PubMed2003

Binding of copper(II) ions to the polyproline II helices of PEVK modules of the giant elastic protein titin as revealed by ESI-MS, CD, and NMR.

Titin, a family of giant elastic proteins, constitutes an elastic sarcomere matrix in striated muscle. In the I-band region of the sarcomere, the titin PEVK segment acts as a molecular spring to generate elasticity as well as sites of adhesion with parallel thin filaments. Previously, we reported that PEVK consists of tandem repeats of 28 residue modules and that the "polyproline II-coil" motif is the fundamental conformational motif of the PEVK module. In order to characterize the factors that may affect and alter the PPII-coil conformational motifs, we have initiated a systematic study of the interaction with divalent cations (Cu2+, Ca2+, Zn2+, and Ni2+) and a conformational profile of PEVK peptides (a representative 28-mer peptide PR: PEPPKEVVPEKKAPVAPPKKPEVPPVKV and its subfragments PR1: kvPEPPKEVVPE, PR2: VPEKKAPVAPPK, PR3: KPEVPPVKV). UV-Vis absorption difference spectra and CD spectra showed that Cu2+ bound to PR1 with high affinity (20 microM), while its binding to PR2 and PR3 as well as the binding of other cations to all four peptides were of lower affinity (>100 microM). Conformational studies by CD revealed that Cu2+ binding to PR1 resulted in a polyproline II to turn transition up to a 1:2 PR1/Cu2+ ratio and a coil to turn transition at higher Cu2+ concentration. ESI-MS provided the stoichiometry of PEVK peptide-Cu2+ complexes at both low and high ion strength, confirming the specific high affinity binding of Cu2+ to PR1 and PR. Furthermore, NMR and ESI-MS/MS fragmentation analysis elucidated the binding sites of the PEVK peptide-Cu2+ complexes at (-2)KVPE2, 8VPE10, 13APV15, and 22EVP24. A potential application of Cu2+ binding in peptide sequencing by mass spectrometry was also revealed. We conclude that Cu2+ binds and bends PEVK peptides to a beta-turn-like structure at specific sites. The specific targeting of Cu2+ towards PPII is likely to be of significant value in elucidating the roles of PPII in titin elasticity as well as in interactions of proline-rich proteins.

Amino Acid Sequence↗
PubMed2006

Association of calcineurin with mitochondrial proteins.

Using mouse hearts from Swiss Webster mice, calcineurin was immunoprecipitated using commercially available anti-calcineurin antibody and the resulting complex analyzed by using sodium dodecyl sulfate-gel electrophoresis with silver staining. Distinct proteins were observed and subjected to in situ trypsin digestion followed by extraction of the resulting peptides. Peptides from each protein band were loaded onto a target for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and analyzed. The resulting peptide mass spectrum was compared with the Mascot and Protein Prospector databases and resulted in the specific identification of heart mitochondrial proteins, specifically Mn-superoxide dismutase (SOD), aconitase (ACN), and malate dehydrogenase (MDH). Each of the three mitochondrial enzymes was identified with approximately 15-25% sequence coverage and all with statistical significance (P < 0.05) according to the Mascot database search engine. Tandem mass spectrometry analysis of the peptide fragmentation spectra confirmed the identification of these protein partners and also yielded the identification of mitochondrial isocitrate dehydrogenase (ICDH) as another protein in the immunoprecipitated complex. Using antibody preparations against Mn-SOD, ACN, and ICDH showed the presence of calcineurin and each of the three proteins in the immunoprecipitated complex by Western slot blotting. The activity of ACN, but not MDH or ICDH, was enhanced after incubation with calcineurin indicating one possible regulatory function for the complex. The mitochondrial forms of Mn-SOD, ACN, MDH, and ICDH were identified as partner proteins of calcineurin with all the proteins present in a single multiprotein complex.

Aconitate Hydratase↗
PubMed1984

The ultrastructure of experimental arthrosis in dogs.

Experimental arthrosis was induced in previously healthy joints in a group of dogs by injection of fluid aspirated from another joint of the same animal previously damaged by trauma under sterile conditions. Using electron microscopy progressive degenerative changes were observed at the surface of the joint, in the extracellular matrix, in the chondrocytes and in the pericellular band. The changes increased following serial injections of the joint fluid. In another series, the joints were injected either with the centrifuged concentrate or the supernatant fluid and a comparison made of the contrasting effects upon the cellular and extracellular structures.

Animals↗
PubMed1992

Appearance of an intra-acrosomal antigen during the terminal step of spermiogenesis in the rat.

In a survey of sperm antigens in the rat, a new intra-acrosomal antigen was found using a monoclonal antibody MC41 raised against rat epididymal spermatozoa. The MC41 was immunoglobulin G1 and recognized spermatozoa from rat, mouse and hamster. Indirect immunofluorescence with MC41 specifically stained the crescent region of the anterior acrosome of the sperm head. Immuno-gold electron microscopy demonstrated that the antigen was localized within the acrosomal matrix. Immunoblot study showed that MC41 recognized a band of approximately 165,000 dalton in the extract of rat sperm from the cauda epididymidis. Immunohistochemistry with MC41 demonstrated that the antigen was first detected in approximately step-2 spermatids, and distributed over the entire cytoplasmic region of spermatids from step 2 to early step 19. The head region became strongly stained in late step-19 spermatids and then in mature spermatozoa. Distinct immunostaining was not found in the developing acrosome of spermatids throughout spermiogenesis. These results suggest that the MC41 antigen is a unique intra-acrosomal antigen which is accumulated into the acrosome during the terminal step of spermiogenesis.

Acrosome↗
PubMed1989

The binding pattern of peanut lectin associated with sclerotome migration and the formation of the vertebral axis in the chick embryo.

Lectins have been used extensively to detect changes in carbohydrate moieties on the surfaces of embryonic cells during early development. Peanut agglutinin (PNA) in particular has been used to investigate changes related to cell differentiation. PNA has also been used to differentiate between the rostral and caudal sclerotome halves which have been shown to be functionally different, with neural crest cells and neurites traversing only the rostral half during their migration. In this study, we have sectioned and stained chick embryos between 3 and 8 days of age with PNA to examine the distribution of PNA binding sites associated with the vertebral column during this period and also to determine the fates of the rostral and caudal sclerotome halves. Ultrastructural localisation of PNA-gold conjugate showed that binding sites for this lectin were present intracellularly and extracellularly both on cell surfaces and in the matrix. At the light microscope level, a clear banding pattern emerged after staining with PNA which consisted of alternating light and dark staining along the entire length of the vertebral axis of the embryo. In the younger embryos, a simple banding pattern emerged where the rostral sclerotome half of each segment stained only lightly while the caudal half stained darkly. This banding pattern was present throughout the 6 day period of development and could be traced continuously but grew more complex as the sclerotome cells migrated to surround the notochord and neural tube and as the dorsal root ganglia developed. The rostral sclerotome half was found to contribute to the caudal part of one vertebral body and its neural arch, while the caudal sclerotome half was found to contribute to the intervertebral disc, the rostral half of the next caudal vertebra, and part of its neural arch.

Animals↗
PubMed1987

Colorimetric-detected DNA sequencing.

A sensitive, colorimetric method for visualizing the band pattern of DNA sequencing reaction is described. The enzymatic incorporation of radioactive nucleotides commonly used for the band detection is replaced by biotin conjugated to the 5'-terminus of a synthetic oligonucleotide by chemical synthesis. The oligonucleotide so labeled is used as a primer for dideoxy DNA sequencing in a primer extension reaction. The products of the sequencing reactions are analyzed on a denaturing polyacrylamide gel using the direct blotting electrophoresis technique. This technique makes it possible to transfer the band pattern during the electrophoresis onto an immobilizing matrix, on which it is made visible by an enzymatic reaction in less than 3 h. This biotin-based detection method is so sensitive that the sequencing reactions can be performed under the same conditions and concentrations as those for the radioactive detection.

Bacterial Proteins↗
PubMed1992

Skew orientation of biological samples Anacystis nidulans cyanobacteria and their fragments in a polymer matrix.

Anacystis nidulans cyanobacteria and their fragments embedded in unstretched, uniaxial and skew (two axes of stretching forming an angle of 40 degrees) stretched poly(vinyl alcohol) films have been investigated. Polarized absorption spectra for uniaxial and skew stretching samples were measured. Both unoriented and oriented samples were photographed under fluorescence microscope. In skew samples a high degree of cell orientation was reached. Skew deformation of polymer matrix compared to one axis stretching provides better band resolution in polarized absorption spectra of Anacystis nidulans samples. The shapes of absorption components measured in respect to the first and second axis of stretching are different which gives the opportunity to investigate position of various group of chlorophyll molecules in membrane.

Cell Membrane↗
PubMed2005

Experimental and theoretical study of the atmospherically important O2-H2O complex.

The theoretically predicted water-oxygen van der Waals adduct has been experimentally confirmed by vibrational characterization using matrix isolation spectroscopic studies at 10 K. Vibrational bands for asymmetric and symmetric OH-stretching for this adduct have been found at 3728 cm(-1) and 3639 cm(-1), respectively. Theoretical calculations performed with Gaussian 98 software at the MP2/6-311++G(2d,2p) level of theory support the alternative structure of the hydrated complex proposed by this study.

Atmosphere↗