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 739 records · Page 41Linked to original sources
PubMed1991

Murine interleukin 5 receptor isolated by immunoaffinity chromatography: comparison of determined N-terminal sequence and deduced primary sequence from cDNA and implication of a role of the intracytoplasmic domain.

The murine interleukin 5 receptor (IL-5R) was identified by utilizing an immobilized IL-5 and an immobilized monoclonal antibody against the murein IL-5R (designated H7 mAb). The H7 mAb immunoaffinity-purified materials from the extract of cell-surface radioiodinated T88-M cells (an IL-5-dependent early B cell line) using 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS) were reacted with an immobilized IL-5 matrix. SDS-PAGE of the adsorbed fraction revealed a single band at approximately 60 kDa. The binding of the 60 kDa protein to the immobilized IL-5 matrix was inhibited by the excess IL-5. The CHAPS-extract depleted of the 60 kDa protein by the absorption with H7 mAb did not contain any IL-5 binding proteins. Immunoaffinity procedure provided a final 7400-fold purification, based on an estimation of the content of the 60 kDa protein (approximate purity: 20%) from the silver-stained pattern of SDS-PAGE. Actin was copurified with the 60 kDa protein at an approximate ratio of 1:1, suggesting that the intracytoplasmic domain of the IL-5R may interact with actin. Furthermore, soluble IL-5R (molecular mass: 50 kDa) was purified by the H7 mAb-immunoaffinity chromatography. The purified soluble IL-5R was capable of inhibiting the binding of IL-5 to T88-M cells. Preparative SDS-PAGE followed by electroblotting onto a membrane permitted the determination of the N-terminal sequence of the IL-5R. The determined N-terminal sequence of the IL-5R and the deduced primary sequence from recently isolated cDNA were compared.

Actins↗
PubMed2002

Three-dimensional helical coiling structures and band patterns of hydrous metaphase chromosomes observed by low vacuum scanning electron microscopy.

Helical coiling structures and band patterns of hydrous metaphase chromosomes were documented three-dimensionally by low vacuum scanning electron microscopy (SEM). Fixed or unfixed isolated Chinese hamster metaphase chromosomes were stained with platinum blue (Pt blue) and observed in the backscattered electron mode for low vacuum SEM without any hypotonic treatment or drying processes. Fibrous structures were shown both in the fixed and unfixed hydrous chromosomes; helical chromatid coils and their subcoils were clarified especially in the fixed chromosomes having contrasting alternative bands of light and darkness, while the translucent perichromosomal matrix and compact fibrous structures were recognized in the unfixed chromosomes. The helical coils were more clearly represented in a loosened chromatid of metaphase chromosomes. Treatment with a tris-HCl buffer solution and Pt blue staining in a hydrous condition successfully produced banding patterns similar to G-bands on metaphase chromosomes. These banded chromosomes observed by low vacuum SEM were also analyzed stereoscopically by field emission SEM after critical point drying. These findings indicate that: 1) native or unfixed chromosomes maintain the compact arrangement of high-order helical structures covered with the peri-chromosomal matrix; 2) helical coiling appearances of chromatids frequently observed in previous papers might be caused by loosening of the final level of the high-order structure of the metaphase chromosome; and 3) banding patterns might be produced by the rearrangement or reorganization of chromatin fibers at the 30 nm fiber level after the extraction of some chromosomal components including the peri- or intra-chromosomal materials during the banding procedure.

Animals↗
PubMed1992

Symmetrically banded collagen fibrils: observations on a new cross striation pattern in vivo.

Collagen fibrils with a symmetric banding pattern, an as yet overlooked component of the extracellular matrix, were found in the reticular layer of the basement membrane of human sebaceous glands. In longitudinal sections this newly described banding pattern is D-periodic (D = 67 nm) resembling the period length of native type collagen fibrils. In cross sections the symmetrically banded fibrils are irregularly outlined. The period length and the symmetric banding pattern led to the assumption that collagen molecules are staggered by the distance D, similar to native type collagen fibrils, but are arranged antiparallel. This hypothesis was tested by antiparallel superposing transparent photocopies of native type fibrils. In addition, schematic drawings of the cross striation pattern of native type fibrils were superposed in reverse directions by means of computerized image-manipulation. A model of molecular alignment was evolved from these experiments, which is characterized by two features: 1) pairs of antiparallel collagen molecules are D-staggered and 2) the two molecules of a pair are slightly shifted from precise register. The proposed model is the only one correlating with the data obtained from direct measurements on symmetrically cross striated fibrils. The fibrils described in the present study represent a supramolecular aggregate of collagen previously not observed in vivo.

Basement Membrane↗
PubMed1998

[FTIR study on structure of pearl and nacre of mollusk shell].

Pearl and nacre of mollusk shell (Hyriopsis cumingii) were studied with high resolution Fourier transformation infrared spectroscopy (FTIR) and X-ray diffraction (XRD). The results of X-ray diffraction indicate that the samples are still aragonite after thermal treatment at 160 degrees C for 5hr, however, the significant variations of peak position and band width of FTIR spectra reveal the interaction between organic matrix and inorganic crystal in biomineralized materials. The variations of spectra were studied by a curve-fitting algorithm and the band related to the interaction is revealed.

Animals↗
PubMed1992

Casein kinase II protein kinase is bound to lamina-matrix and phosphorylates lamin-like protein in isolated pea nuclei.

A casein kinase II (CK II)-like protein kinase was identified and partially isolated from a purified envelope-matrix fraction of pea (Pisum sativum L.) nuclei. When [gamma-32P]ATP was directly added to the envelope-matrix preparation, the three most heavily labeled protein bands had molecular masses near 71, 48, and 46 kDa. Protein kinases were removed from the preparation by sequential extraction with Triton X-100, EGTA, 0.3 M NaCl, and a pH 10.5 buffer, but an active kinase still remained bound to the remaining lamina-matrix fraction after these treatments. This kinase had properties resembling CK II kinases previously characterized from animal and plant sources: it preferred casein as an artificial substrate, could use GTP as efficiently as ATP as the phosphoryl donor, was stimulated by spermine, was calcium independent, and had a catalytic subunit of 36 kDa. Some animal and plant CK II kinases have regulatory subunits near 29 kDa, and a lamina-matrix-bound protein of this molecular mass was recognized on immunoblot by anti-Drosophila CK II polyclonal antibodies. Also found associated with the envelope-matrix fraction of pea nuclei were p34cdc2-like and Ca(2+)-dependent protein kinases, but their properties could not account for the protein kinase activity bound to the lamina. The 71-kDa substrate of the CK II-like kinase was lamin A-like, both in its molecular mass and in its cross-reactivity with anti-intermediate filament antibodies. Lamin phosphorylation is considered a crucial early step in the entry of cells into mitosis, so lamina-bound CK II kinases may be important control points for cellular proliferation.

Amino Acid Sequence↗
PubMed2004

Triplet diphenylcarbenes protected by o-Aryl groups.

Diphenyldiazomethanes (2a-N(2)) having phenyl groups at the ortho positions were prepared and the corresponding diphenylcarbenes (2a) photolytically generated from them were characterized not only by the traditional product analysis method but also by ESR and UV/vis spectroscopy in a rigid organic matrix at low temperature and in laser flash photolysis in solution at room temperature. Product analysis indicated that fluorenes 4a are formed almost exclusively. Fluorene is most likely produced by the attack of singlet carbene (1)2a on an ortho carbon of the phenyl substituent to generate isofluorene, followed by 1,5-H shift. Irradiation of 2a-N(2) in a 2-methyltetrahydrofuran (2-MTHF) matrix at 77 K gave ESR signals ascribable to triplet carbenes ((3)2a). UV/vis spectra of (3)2a were obtained by irradiating 2a-N(2) under identical conditions. However, laser flash photolysis (LFP) of 2a-N(2) in degassed benzene at room temperature showed transient absorption bands completely different from those observed in photolysis in the 2-MTHF matrix at 77 K. The transient band decayed in first-order with a rate constant of 7.6 x 10(4) s(-1), which was not retarded by deuterium substitution of o-phenyl hydrogens. Essentially the same transient band was observed in LFP of fluorene 4a. The LFP of 2a-N(2) in nondegassed benzene gave transient absorption bands ascribable to triplet carbene (3)2a and the corresponding carbonyl oxide. The quenching rate constant of (3)2a by oxygen and the lifetime of (3)2a in the absence of oxygen were estimated by plotting the observed pseudo-first-order rate constant of the formation of the carbonyl oxide against the concentration of oxygen. They were 1.9 x 10(7) M(-1)s(-1) and 16 micros, respectively. Similar studies with diphenyldiazomethanes having a series of substituents (4-Ph, 3,5-(CF(3))(2), and 2-F) on the ortho-phenyl rings gave essentially identical results, indicating that those substituents exhibit little effect on overall reaction pathway. From those studies, it is suggested that triplet carbenes (3)2 are also trapped by the ortho-phenyl ring to give eventually fluorenes.

Journal Article↗
PubMed1999

Polycyclic aromatic hydrocarbons and the diffuse interstellar bands: a survey.

We discuss the proposal relating the origin of some of the diffuse interstellar bands (DIBs) to neutral and ionized polycyclic aromatic hydrocarbons (PAHs) present in interstellar clouds. Laboratory spectra of several PAHs, isolated at low temperature in inert gas matrices, are compared with the spectra of five reddened early-type stars selected from an extensive set of astronomical spectra. From this comparison, it is concluded that PAH ions are good candidates to explain some of the DIBS. Unambiguous assignments are difficult, however, because of the shift in wavelengths and the band broadening induced in the laboratory spectra by the solid matrix. This situation is illustrated by a comparison with the gas-phase spectra made available recently for two PAH ions. Definitive band assignments and, ultimately, the test of the proposal that PAH ions carry some of the DIBs must await the availability of a larger set of gas-phase measurements in the laboratory. The present assessment offers a guideline for future laboratory experiments by allowing the preselection of promising PAH molecules to be studied in jet expansions.

Astronomical Phenomena↗
PubMed2004

N-linked oligosaccharide analysis of glycoprotein bands from isoelectric focusing gels.

Glycoproteins often display a complex isoelectric focusing profile because of the presence of negatively charged carbohydrates, such as sialic acid, phosphorylated mannose, and sulfated GalNAc. Until now, understanding the role of these charged carbohydrates in determining the isoelectric focusing profile has been limited to observing pattern shifts following complete removal of the sugars in question. We have developed a simple and sensitive method for analyzing N-linked oligosaccharides from the individual isoelectric focusing bands of a glycoprotein using recombinant human thyroid-stimulating hormone as a model system. N-linked oligosaccharides were released and profiled from individual bands following electroblotting of isoelectric focusing gels. As might be predicted, high-pH anion-exchange chromatography-pulsed amperometric detection and matrix-assisted laser desorption/ionization-time of flight analyses indicated that the bands that migrated closer to the positive electrode contained more sialylated N-linked oligosaccharides. The sialic acid content of these bands correlated with that predicted from the corresponding oligosaccharide analyses.

Chromatography, Ion Exchange↗
PubMed1997

Synthesis, secretion, degradation, and fate of ameloblastin during the matrix formation stage of the rat incisor as shown by immunocytochemistry and immunochemistry using region-specific antibodies.

Rat ameloblastin is a recently cloned tooth-specific enamel matrix protein containing 422 amino acid residues. We investigated the expression of this protein during the matrix formation stage of the rat incisor immunohistochemically and immunochemically, using anti-synthetic peptide antibodies that recognize residues 27-47 (Nt), 98-107 (M-1), 224-232 (M-2), 386-399 (M-3), and 406-419 (Ct) of ameloblastin. Immunohistochemical preparations using antibodies Nt and M-1 stained the Golgi apparatus and secretory granules of the secretory ameloblast and the entire thickness of the enamel matrix. Only M-1 intensely stained the peripheral region of the enamel rods. Immunostained protein bands were observed near 65, 55, and below 22 kD. Immunohistochemical preparations using antibodies M-2 and Ct stained the Golgi apparatus and secretory granules of the ameloblast and the immature enamel adjacent to the secretion sites, but not deeper enamel layers. Immunostaining using M-2 and Ct revealed protein bands near 65 and 40-56 kD, and 65, 55, 48, 36, and 25 kD, respectively. M-3 stained the cis side of the Golgi apparatus but not the enamel matrix. This antibody recognized a protein band near 55 kD, but none larger. After brefeldin A treatment, immunoreaction of the 55-kD protein band intensified, and dilated cisternae of rER of the secretory ameloblast contained immunoreactive material irrespective of the antibodies used. These data indicate that ameloblastin is synthesized as a 55-kD core protein and then is post-translationally modified with O-linked oligosaccharides to become the 65-kD secretory form. Initial cleavages of the 65-kD protein generate N-terminal polypeptides, some of which concentrate in the prism sheath, and C-terminal polypeptides, which are rapidly degraded and lost from the enamel matrix soon after secretion.

Ameloblasts↗
PubMed1989

Collagen and proteoglycan in a sea urchin ligament with mutable mechanical properties.

The "problematic ligament" of sea urchins is a connective tissue which crosses the ball-and-socket joint between spine and body wall. The problem of this ligament is that it is composed of parallel collagen fibrils, yet normally undergoes rapid and dramatic alterations in mechanical properties and in length. Previous work has suggested that the collagen fibrils of the ligament are able to slide past one another during length changes but are inhibited from sliding when the ligament is in "catch". In this model of the ligament both the collagen fibrils and the interfibrillar matrix are mechanically important. We have found that the collagen fibrils of the spine ligament of the pencil urchin Eucidaris tribuloides are discontinuous and end by tapering within the body of the ligament. Intact fibrils that have been isolated from the ligament vary by more than an order of magnitude in length and in radius but have a constant length/radius (aspect) ratio of about 5,300. This is the first determination of the aspect ratio of collagen fibrils from any source. The constant aspect ratio of the fibrils is consistent with their functioning as the discontinuous fiber phase in a fiber-reinforced composite material, while the high value of the aspect ratio indicates that the nonfibrillar matrix, which must act to transfer stress between fibrils, can produce a stiff and strong ligament even if it is several orders of magnitude weaker and more compliant than the fibrils. Moreover, the tensile properties of the ligament may be determined by the properties of the matrix. A prominent component of the interfibrillar matrix is a proteoglycan which associates with specific bands at the surface of the collagen fibrils through noncovalent binding of its core protein. The glycosaminoglycan moiety of this proteoglycan is partly comprised of chondroitin sulfate/dermatan sulfate polymers. These results are consistent with the "sliding fibril" hypothesis and suggest that the proteoglycan may be an important component of the stress-transfer matrix.

Animals↗
PubMed1999

Characterization of a novel human surface molecule selectively expressed by mature thymocytes, activated T cells and subsets of T cell lymphomas.

We have previously characterized mouse H4 (mH4), a surface glycoprotein recognized by the C398.4A monoclonal antibody. We now show that C398.4A also binds its human putative homolog (hpH4). Both hpH4 and mH4 (1) are selectively expressed by activated T cells and mature thymocytes, (2) are disulfide-linked dimers of two chains (29/37 kDa in humans, 25/29 kDa in mice), whose N-deglycosylation produces a single band at 20 - 21 kDa, and (3) display a low association with CD4 and the TCR. The expression pattern of hpH4 and its biochemical features showed that it is different from other known activation molecules, and this was confirmed when analysis of the tryptic digest of the hpH4 29-kDa band by peptide mass searching using matrix-assisted laser desorption ionization mass spectrometry did not reveal any significant homology with other molecules. In normal lymphoid tissue, hpH4 is expressed by T cells located at the periphery of lymph node germinal centers and paracortical areas. In T cell neoplasia, expression of hpH4 clusters with a subset of peripheral T cell lymphomas with a large-cell component, and with cases of angioimmunoblastic T cell lymphomas. Overall, these data provide evidence for a novel T cell activation molecule that could help in the phenotypic categorization of T cell malignancies.

Animals↗
PubMed1988

Improved transfer of high molecular weight proteins using fabric-reinforced soft polyacrylamide gels.

Rapid transfer of electrophoretically separated, high molecular weight proteins from fabric-reinforced, soft, low-concentration polyacrylamide gels (3.5%T, 2.6%C) is described. Polyester fabrics proved useful for gel reinforcement during vertical slab gel electrophoresis. The fabric-reinforced gel retains its dimension during transfer, equilibration and drying, facilitating comparison of protein bands in the separation gel and transfer matrix.

Collodion↗
PubMed1996

Enhanced in situ gel digestion of electrophoretically separated proteins with automated peptide elution onto mini reversed-phase columns.

An improved method for the generation and automated isolation of internal peptides by in situ gel digestion of electrophoretically separated proteins is described. To enhance the sensitivity of the method, and to reduce the amount of sample handling steps, we have automated the extraction procedure of peptides after protein cleavage in a sodium dodecyl sulfate (SDS) gel matrix. The excised protein-containing polyacrylamide bands or spots are first minced to defined particles of about 30 microns. After in situ gel digestion, the gel slurry is transferred into a mini reversed-phase column-funnel assembly in the sample loading station of the Hewlett-Packard protein sequencer. Applying nitrogen pressure elutes peptides from the gel slurry onto the reversed-phase material. The mini reversed-phase column is then placed in an in-line column adapter and connected to a micropreparative high performance liquid chromatography (HPLC) column, where separation of the peptides under standard conditions is achieved. In the work described here complete digestions and excellent peptide recoveries allowed the generation of extensive internal sequence information from low picomole amounts of proteins. The method has been routinely applied in both laboratories for two years.

Acrylic Resins↗
PubMed1994

Sculpting proteins interactively: continual energy minimization embedded in a graphical modeling system.

We describe a new paradigm for modeling proteins in interactive computer graphics systems--continual maintenance of a physically valid representation, combined with direct user control and visualization. This is achieved by a fast algorithm for energy minimization, capable of real-time performance on all atoms of a small protein, plus graphically specified user tugs. The modeling system, called Sculpt, rigidly constrains bond lengths, bond angles, and planar groups (similar to existing interactive modeling programs), while it applies elastic restraints to minimize the potential energy due to torsions, hydrogen bonds, and van der Waals and electrostatic interactions (similar to existing batch minimization programs), and user-specified springs. The graphical interface can show bad and/or favorable contacts, and individual energy terms can be turned on or off to determine their effects and interactions. Sculpt finds a local minimum of the total energy that satisfies all the constraints using an augmented Lagrange-multiplier method; calculation time increases only linearly with the number of atoms because the matrix of constraint gradients is sparse and banded. On a 100-MHz MIPS R4000 processor (Silicon Graphics Indigo), Sculpt achieves 11 updates per second on a 20-residue fragment and 2 updates per second on an 80-residue protein, using all atoms except non-H-bonding hydrogens, and without electrostatic interactions. Applications of Sculpt are described: to reverse the direction of bundle packing in a designed 4-helix bundle protein, to fold up a 2-stranded beta-ribbon into an approximate beta-barrel, and to design the sequence and conformation of a 30-residue peptide that mimics one partner of a protein subunit interaction. Computer models that are both interactive and physically realistic (within the limitations of a given force field) have 2 significant advantages: (1) they make feasible the modeling of very large changes (such as needed for de novo design), and (2) they help the user understand how different energy terms interact to stabilize a given conformation. The Sculpt paradigm combines many of the best features of interactive graphical modeling, energy minimization, and actual physical models, and we propose it as an especially productive way to use current and future increases in computer speed.

Amino Acid Sequence↗
PubMed1993

Substrate-gel electrophoresis for composition and molecular weight of proteinases or proteinaceous proteinase inhibitors.

A rapid, sensitive, and generally applicable substrate-sodium dodecyl sulfate-polyacrylamide gel electrophoresis method for detection of proteinases or proteinaceous protease inhibitors in biological preparations is described. Electrophoretic separation of proteinases or proteinaceous proteinase inhibitors in the sample using sodium dodecyl sulfate-polyacrylamide gel slabs is followed by immersion of the gel in (1) a protein substrate solution for detection of proteinases or (2) an appropriate proteinase solution, and then in a protein substrate solution for detection of proteinase inhibitors. Some advantages of the reported method over previously described techniques that incorporate substrate into the gel matrix are: (1) the development of bioactive bands, as well as staining and washing, is accomplished more quickly, i.e., 4 to 6 h; (2) the trailing of proteolysis which often appears in copolymerized substrate systems is eliminated; (3) the method is applicable to assay at pH values other than those used for electrophoresis; (4) molecular weight markers can be visualized on the same gels; (5) proteinaceous proteinase inhibitors can also be examined in the biological samples; and (6) the sensitivity is several times higher than that of former assays.

Animals↗
PubMed1995

Genetic relationships among strains of Xylella fastidiosa from RAPD-PCR data.

Genetic relationships among 11 Xylella fastidiosa strains isolated from mulberry, almond, ragweed, grape, plum, elm, and citrus were determined by random amplified polymorphic DNA (RAPD). Twenty-two 10-base primers amplified a total of 77 discrete polymorphic bands. Phenetic analysis based on a similarity matrix corresponded well with previous reports on X. fastidiosa RFLP-based similarity relationships, indicating that RAPD-PCR amplification products can be used as a reliable indicator of genetic distance in X. fastidiosa. Cladistic analysis suggests the existence of five groups of X. fastidiosa: the citrus group, the plum-elm group, the grape-ragweed group, the almond group, and the mulberry group.

Base Sequence↗
PubMed1996

Evidence for genomic changes in transgenic rice (Oryza sativa L.) recovered from protoplasts.

The occurrence of genomic modifications in transgenic rice plants recovered from protoplasts and their transmission to the self-pollination progeny has been verified with the random amplified polymorphic DNA (RAPD) approach. The plant was the Indica-type rice (Oryza sativa L.) cultivar Chinsurah Boro II. The analysed material was: (1) microspore-derived embryogenic rice cells grown in suspension culture, (2) transgenic plants recovered from protoplasts produced from the cultured cells and (3) the self-pollination progeny (two successive generations) of the transgenic plants. DNA purified from samples of these materials was PCR-amplified with different random oligonucleotide primers and the amplification products were analysed by agarose gel electrophoresis. Band polymorphism was scored and used in band-sharing analyses to produce a similarity matrix. Relationships among the analysed genomes were expressed in a dendrogram. The extensive DNA changes evidenced in cultured cells demonstrate the occurrence of somaclonal variation in the material used to produce protoplasts for gene transfer. Quantitatively reduced DNA changes were also found in the resulting transgenic plants and in their self-pollination progenies. While confirming the stability of the foreign gene in transgenic plants, this work gives molecular evidence for the occurrence of stable genomic changes in transgenic plants and points to in vitro cell culture as the causative agent. RAPDs are shown to be a convenient tool to detect and estimate the phenomenon at the molecular level. The methodology is also proposed as a fast tool to select those transgenic individuals that retain the most balanced genomic structure and to control the result of back-crosses planned to restore the original genome.

DNA, Plant↗
PubMed1994

Separation of proteins using cetyltrimethylammonium bromide discontinuous gel electrophoresis.

The gel electrophoresis system presented here allows the separation of proteins with the concomitant retention of detectable native activities. The system, referred to as CAT gel electrophoresis, uses the detergent cetyltrimethylammonium bromide in combination with a discontinuous gel matrix to resolve protein mixtures into discrete bands. Many proteins retain detectable levels of native activity after CAT electrophoresis, and gel bands can be easily identified using assays based on specific enzymatic activities or binding characteristics. The ability to identify protein bands based on Both M(r) and activity in a single gel makes the CAT system a powerful adjunct to existing biochemical techniques.

Biotechnology↗