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PubMed2004

Snake venomics: characterization of protein families in Sistrurus barbouri venom by cysteine mapping, N-terminal sequencing, and tandem mass spectrometry analysis.

The protein composition of the crude venom of Sistrurus barbouri was analyzed by two-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis. Proteins were separated by reversed phase high-performance liquid chromatography and characterized by N-terminal sequence analysis. The molecular mass and number of cysteine residues of the purified proteins were determined by matrix-associated laser desorption/ionization-time of flight mass spectrometry. Selected protein bands were subjected to in-gel tryptic digestion and peptide mass fingerprinting. Analysis of the tandem mass spectrometry spectra of selected doubly-charged peptide ions was done by collision-induced dissociation in a quadrupole-linear ion trap instrument. Our results show that the venom proteome of the pigmy rattlesnake S. barbouri is composed of proteins belonging to a few protein families, which can be structurally characterized by their disulfide bond contents.

Amino Acid Sequence↗
PubMed1988

Human KRAS oncogene expression in meningioma.

Expression of 16 oncogenes was investigated in a series of human meningiomas showing a normal chromosome complement or the characteristic monosomy 22 but no structural aberrations detectable by banding analysis. By dot hybridization, the only expressed sequence detected was KRAS. The expression was elevated approximately 6--8-fold in comparison to matrix tissue (meninges) and to fibroblasts of the corresponding patient. Northern blot analysis displayed the typical banding pattern and an 8--10-fold overexpression. DNA analysis did not reveal gene amplification or major rearrangements in the KRAS gene structure.

Blotting, Northern↗
PubMed1983

Multivariate analysis of EEG coherence: stability of the metric, individual differences in patterning and response to arousal.

When coherence is computed among all pairs of a multichannel EEG, the resultant matrix can be de-structured with conventional multivariate analysis procedures to characterize the patterning of electrophysiologic information at each frequency band of the EEG across brain regions. Six right-handed young men had EEG data recorded from left and right frontal, temporal, parietal, and occipital locations during three visits to the laboratory at one week intervals. During each session, data were recorded during a relaxation period, an alert resting period, and as loud white noise was presented. Factor analysis of coherence matrices showed a model pattern of a large posterior factor and an anterior factor, both of which were right-lateralized, plus a residual factor that was most often left-lateralized. Four of the six men showed this pattern on each occasion, particularly for the delta and the theta bands. Two men showed variant patterns, which were also stable over time. A priori de-structuring of the matrix into partial multiple intrahemispheric and inter-hemispheric coherences also showed generally higher coherences on the right side, with the exception of left occipital inter-hemispheric values. Effects of arousal manipulations were not striking, but the factor patterns suggested increases in right hemisphere coherence for the alpha and beta bands during high arousal.

Adult↗
PubMed2000

Mini review: form and function in the human interphase chromosome.

A key feature of interphase chromosomes is their compaction into discrete "territories" in the nucleus. In this review, we focus on the compartmentalization of the genome conferred by this organization and evaluate our current understanding of the role of large-scale chromatin folding in the regulation of gene expression. We examine evidence for the hypothesis that transcription occurs at the external surfaces of chromosomes and follow its evolution to include transcription at the surfaces of chromatin-rich domains within chromosomes. We also present prevailing views regarding the details of large-scale chromatin folding and the functional relationship between chromatin and the enigmatic nuclear matrix.

Chromatin↗
PubMed2005

Edge currents in superconductors with a broken time-reversal symmetry.

We analyze edge currents and edge bands at the surface of a time-reversal symmetry breaking dx2-y2 + id(xy) superconductor. We show that the currents have large Friedel oscillations with two interfering frequencies: square root of 2kF from subgap states, and 2kF from the continuum. The results are based independently on a self-consistent slave-boson mean-field theory for the t-J model on a triangular lattice, and on a T-matrix scattering theory calculation. The shape of the edge-state band, as well as the particular frequency square root of 2kF of the Friedel oscillations, are attributes unique for the dx2-y2 + id(xy) case, and may be used as a fingerprint for its identification. Extensions to different time-reversal symmetry breaking superconductors can be achieved within the same approach.

Journal Article↗
PubMed1999

Peptide mapping of proteins in cerebrospinal fluid utilizing a rapid preparative two-dimensional electrophoretic procedure and matrix-assisted laser desorption/ionization mass spectrometry.

A quick two-step procedure involving liquid phase isoelectric focusing in the Rotofor cell in combination with electroelution in the Mini whole cell gel eluter has been used for purification of proteins from human cerebrospinal fluid (CSF). Fractions, each highly enriched in a single protein band and virtually free of other proteins, were selected for characterization by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOFMS). Six CSF proteins, transferrin, alpha1-acid-glycoprotein, Zn-alpha2-glycoprotein, apolipoprotein A1, apolipoprotein E and beta-trace were identified by MALDI-TOFMS analysis of the tryptic digests. These results demonstrate that the combination of liquid phase IEF and electroelution is a rapid preparative two-dimensional separation which can provide single proteins of high purity, in yields sufficient for characterization by MALDI-TOFMS. Characterization of such brain-specific proteins in CSF will be useful in the investigation of the pathophysiology of different brain disorders.

Cerebrospinal Fluid Proteins↗
PubMed1995

Extracellular matrix deposition in hypertensive hearts antifibrotic effects of ramipril.

Hypertension induced in rats by suprarenal banding has a blood pressure elevating effect that is accompanied by the occurrence of cardiac hypertrophy and fibrosis. This phenomenon is already present at 2 weeks after banding and persists up to 1.5 years. The increase in cardiac weight is mostly due to the development of fibrosis, since myocytes are only slightly increased in size. The fibrotic tissue consists mainly of fibronectin and collagen and contains numerous cellular elements. The occurrence of fibrosis can be completely inhibited by the administration of the specific ACE inhibiting drug, ramipril, which indicated that angiotensin II may directly stimulate fibroblasts to produce fibronectin and collagen. The antifibrotic effect of ramipril was also present in a low dosage that did not lower blood pressure, confirming the hypothesis that angiotensin II has a direct effect on connective tissue cells and their ability to produce extracellular matrix proteins. The direct effect of the renin-angiotensin system on the activity of interstitial cells was further proven by molecular biology techniques showing an upregulation of transcription for collagen I and III which is prevented by ACE inhibition.

Angiotensin-Converting Enzyme Inhibitors↗
PubMed2006

Characterization and variations of organic parameters in teleost fish endolymph during day-night cycle, starvation and stress conditions.

The aim of the present work was to examine the modifications of the organic composition of fish endolymph under environmental conditions (day-night cycle, starvation and Cl2-stress) known to modify otolith growth. Endolymph electrophoretic patterns were compared. An antibody raised against the trout otolith organic matrix allowed examining the variations of organic matrix precursors in the endolymph under the above conditions. Western blot analysis showed bands around 60-80 kDa. A 50% decrease of immunolabelling was observed during the night whereas increases were seen after starvation (factor 3) or stress (factor 2) suggesting that these variations could be related to the organic matrix deposit. A factor retarding in vitro CaCO3 crystallization (FRC) was shown to co-precipitate with endolymph proteins and its apparent molecular mass (determined by measuring the activity after electro elution of gel electrophoresis) was estimated around 20 kDa. The FRC activity was stable during day-night cycle whereas it decreased by 70% and nearly 100% under starvation and stress respectively. These results suggest that the FRC, although retarding in vitro crystallization, plays a major role in the process of otolith calcification and that the decreases measured after starvation and stress are responsible for the decreases of the otolith growth. The variations of these two parameters (precursors and FRC) could contribute for the changes in the microstructure of the otolith.

Animals↗
PubMed2005

Full-size digital storage phosphor chest radiography: effect of 4K versus 2K matrix size on observer performance in detection of subtle interstitial abnormalities.

PURPOSE: To compare observer performance in the detection of subtle interstitial abnormalities on 3,520 x 3,520 (4K) matrix and 1,760 x 1,760 (2K) matrix full-size digital storage phosphor (DSP) chest radiographs. MATERIALS AND METHODS: Thirty-five 4K DSP chest radiographs with subtle interstitial abnormalities (n=27) or normal lungs (n=8) were processed with a half-band low-pass filter to produce 2K DSP radiographs. Although the actual matrix size of the 2K DSP radiographs remained 4K, the effective matrix size was reduced to 2K. Four chest radiologists independently evaluated full-sized hard-copy of the 4K and 2K DSP radiographs, and scored the presence of interstitial abnormalities for both right and left lungs on a five-point confidence scale. With findings on high-resolution computed tomography as the reference standard, observer performance was evaluated using multireader-multicase receiver operating characteristic (ROC) analysis. RESULTS: The average area under the ROC curve (Az) values for 4K and 2K DSP radiographs were 0.791+/-0.055 and 0.804+/-0.050, respectively. Both individual and averaged Az values showed no statistically significant differences (p>0.05) between 4K and 2K DSP radiographs. CONCLUSION: Observer performance in the detection of subtle interstitial abnormalities on 4K full-size DSP chest radiographs was equivalent to that on 2K full-size DSP chest radiographs.

Humans↗
PubMed1997

Expression and potential role of the extracellular matrix in hepatic ontogenesis: a review.

Studies from a number of laboratories have provided information on the temporal and spatial expression of a variety of extracellular matrix (ECM) components in the developing liver and insight into their potential roles in hepatogenesis. Collagen type IV and laminin are present in the basement membranes of the capsular mesothelium, vascular structures of the portal and hepatic vein branches, and the ductular elements of the developing liver. The mesothelial, vascular, and ductular epithelial cells synthesize laminin and type IV collagen. In contrast, fibronectin and type I collagen are restricted to the adjacent or surrounding interstitium of those ductal and vascular elements, but are not within the basement membrane proper. The hepatic perisinusoidal space (Space of Disse) of the fetal rat develops a delicate extracellular matrix by 12.5 days of gestation, which is characterized by banded collagen fibrils and bundles associated with filamentous and flocculent material. Fibronectin, laminin, and collagen types I, III, and IV are present in the developing perisinusoidal space by this early gestational date, with laminin being the most prevalent component detected. The laminin chains localized to that region in the fetal/neonatal period are alpha 2, beta 1, beta 2, and gamma 1, whereas the alpha 1 chain of laminin is absent from the developing Space of Disse. Similar data have been reported on the laminin phenotype in the perisinusoidal space during hepatic regeneration. Electron microscopy immunohistochemistry studies have demonstrated that the sinusoidal lining cells and hepatocytes synthesize these ECM proteins during hepatogenesis. By 6 to 8 weeks of postnatal life, laminin is not detectable in the perisinusoidal space. Both the transient expression of laminin and the similarity of the laminin chain phenotype expressed in the perisinusoidal space in the developing and regenerating liver suggests a role for this protein in the organization of the hepatic lobule in those forms of hepatic morphogenesis.

Animals↗
PubMed2001

Immunohistochemical localization of amelogenin in human odontogenic tumors, using a polyclonal antibody against bovine amelogenin.

In the present study, we investigated the localization of amelogenin in odontogenic tumors, using an anti-amelogenin polyclonal antibody. In order to make the antibody, antisera against an amelogenin fraction obtained from the enamel matrix of unerupted bovine tooth was raised in rabbits. By Western blot analysis, a main band of 25 kDa and six minor bands (6.8, 12, 18, 20, 23, and 27 kDa) were detected under nonreducing conditions. Immunoreactivity for the amelogenin was observed in ameloblasts and in the immature enamel matrix of 4-day-old rats. In odontogenic tumors, positive reactions for amelogenin were localized in limited areas in adenomatoid odontogenic tumor, calcifying odontogenic cyst, primary intraosseous carcinoma and odontoma. The strongest immunoreactions were shown in enamel matrices in odontomas. Small mineralized foci in epithelial nests showed positive reactions, and a few reactions were observed in epithelium adjacent to the mineralized foci. In calcifying odontogenic cysts, some ghost cells in the lining epithelium were strongly stained. The results indicate that the present antibody for amelogenin is useful for the determination of odontogenic tumors, especially in those in which small mineralized foci are present in the epithelial nests.

Amelogenin↗
PubMed2006

Generation and reactivity of the phenyl cation in cryogenic argon matrices: monitoring the reactions with nitrogen and carbon monoxide directly by IR spectroscopy.

The phenyl cation 1 has been prepared by co-deposition of iodobenzene 6 or bromobenzene 7 with a microwave-induced argon plasma and characterized by IR spectroscopy in cryogenic argon matrices. The cation can clearly be identified by its strongest absorption at 3110 cm(-1) that is rapidly bleached upon visible light irradiation. This characteristic band is observed neither in the conventional photochemistry of 6 or 7 nor in discharge experiments with alkyl halides or chlorobenzene. The latter finding is in line with energetic considerations. According to density functional theory (DFT) computations, the strongest absorption of 1 is caused by a C-H stretching vibration that involves almost entirely the ortho-hydrogens. This is confirmed by isotopic labeling experiments. Co-deposition of halobenzene/N2 mixtures leads to a decrease of the 3110 cm(-1) absorption, whereas several new signals are detected in the 2200-2400 cm(-1) range of the IR spectrum. Annealing of a matrix that contains 1 and 1% N2 leads to an increase of a broad band at 2260 cm(-1) that is assigned to the benzenediazonium ion 2. A sharp signal at 2327 cm(-1) that had previously been assigned to the N-N stretching vibration of 2 is due to molecular nitrogen. The mechanism that triggers the IR activity of N2 is not yet understood. Annealing of a matrix that contains 1 and 0.5% CO leads to an increase of a broad band at 2217 cm(-1) that is considerably stronger than the 2260 cm(-1) absorption of 2. This signal is assigned to the C-O stretching vibration of the benzoyl cation 12, in excellent agreement with previous investigations of 12 in superacidic media. Some consequences of the measured frequencies with regard to bonding in 2 and 12 are discussed.

Journal Article↗
PubMed1981

Age related changes and osteochondrosis in swine articular and epiphyseal cartilage: light ane electron microscopy.

Age related changes and osteochondrosis in swine were studied using light microscopy and electron microscopy in articular cartilage and light microscopy and epiphyseal cartilage of swine from three days to 30 weeks of age. Thickness, cellularity and vascularity of both the epiphyseal and articular cartilage, decreased as the swine aged. Osteochondrotic changes included formation of "plugs" of cartilage indicating localized failure of ossification and separation and space formation in epiphyseal cartilage. Eosinophilic streaks and space formation in epiphyseal cartilage was observed in relation to epiphyseal separation. Electron microscopy showed a continuous fibrillar layer on the surface of the cartilage corresponding to the lamina splendens of light microscopy. This layer increased in the thickness and showed accumulation of amorphous material between the fibrils with aging. In the matrix, the orientation and distribution of the collagen fibers changed with growth and thicker fibers with clear sub banding were more common in older age groups. Also, necrotic cells, glycogen containing bodies and cellular debris were noticed in the matrix of normal cartilage in old animals. Chondrocytes in the younger cartilage showed accumulation of organelles responsible for protein synthesis; while Golgi bodies, vesicles, lysosomes, well developed foot processes and other inclusions were noticed in older cartilage. Cartilage erosions had a clumped and disrupted lamina splendens on the surface and electron lucent patches in the ground substances of the matrix and chondrocyte cytoplasm.

Aging↗
PubMedDate not supplied

Surface topology of collagen fibrils associated with proteoglycans in mouse cornea and sclera.

PURPOSE: To clarify the histological basis for the optical difference in the cornea and sclera, we investigated the surface ultrastructure of D-periodic collagen fibrils. METHODS: The fibril arrangement and topology of D-periodic collagen fibrils from corneas and scleras of mice were examined by transmission and scanning electron microscopy, as well as by atomic force microscopy (AFM). The banding patterns were estimated by densitometry and compared with the profile made by computer simulation from the protein sequence of amino acids. RESULTS: Considerable association of proteoglycans/glycosaminoglycanson XI bands of corneal D-periodic collagen fibrils was seen with ruthenium red staining. Atomic force microscopy imaging showed that the depth of the groove in the D-periodicity of corneal collagen fibrils was shallow compared with that of the sclera. CONCLUSIONS: Corneal collagen fibrils are associated with many extracellular matrix components on both elevated and depressed surfaces of D-periodic bands, which may serve to maintain interfibrillar spaces, resulting in corneal transparency.

Animals↗
PubMed2006

A simple search of TM segments in polytopic membrane protein using matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

Using both high performance liquid chromatography (HPLC) and amino acid sequencing (AAS), we previously analyzed band 3 TM peptide-segments that make up the transmembrane protein structure. However, the HPLC/AAS combination method was highly time-consuming. Matrix-Assisted Laser Desorption Ionization Time-of-Flight (MALDI-TOF) mass spectrometry is used to obtain accurate molecular weight information for proteins/peptides simply and sensitively. We applied the MALDI-TOF mass spectrometry technique to search for TM segments in membrane proteins. In combination with trypsin cleavages after alkali treatments (pH12 or 13) and sample preparation using organic solvents for MALDI-TOF mass spectrometry, we determined the TM segments of band 3 and glycophorin A in erythrocyte membrane. The method can be applied to other polytopic membrane proteins in erythrocyte membrane.

Alkalies↗
PubMed1996

Proton-Induced Tuning of Electrochemical and Photophysical Properties in Mononuclear and Dinuclear Ruthenium Complexes Containing 2,2'-Bis(benzimidazol-2-yl)-4,4'-bipyridine: Synthesis, Molecular Structure, and Mixed-Valence State and Excited-State Properties.

A series of mono- and dinuclear Ru(bpy)(2) complexes (bpy = 2,2'-bipyridine) containing 2,2'-bis(benzimidazol-2-yl)-4,4'-bipyridine (bbbpyH(2)) were prepared. The mononuclear complex [Ru(bpy)(2)(bbbpyH(2))](ClO(4))(2).CH(3)OH.4H(2)O was characterized by an X-ray structure determination. Crystal data are as follows: triclinic, space group P&onemacr;, a = 14.443(4) Å, b = 15.392(4) Å, c = 11.675(2)Å, alpha = 101.44(2) degrees, beta = 107.85(2) degrees, gamma = 96.36(2) degrees, V = 2380(1) Å(3), Z = 2. The coordination geometry of the ruthenium(II) ion is approximately octahedral. The dihedral angle between the two pyridyl rings in bbbpyH(2) is 9.4(3) degrees, which is close to coplanar, in the complex. Mono- and dinuclear complexes exhibit broad charge-transfer absorption bands at 420-520 nm and emission at 660-720 nm in CH(3)CN solution with lifetimes of 200-800 ns at room temperature. Transient difference absorption spectra and resonance Raman (rR) spectra were used to assign the charge-transfer bands in the 420-520 nm region and to identify the lowest excited states. Both absorption and emission spectra are sensitive to solvent and solution pH. Deprotonation of the dinuclear complex raises the energies of the pi orbitals of the bbbpyH(2) ligand, so that they become closer in energy to the pi orbitals of bpy. The intervalence band of [(bpy)(2)Ru(bbbpyH(2))Ru(bpy)(2)](5+)()()is observed at 1200 nm ( epsilon = 170 M(-)(1) cm(-)(1)) in CH(3)CN. The value of the electronic coupling matrix element, H(AB), was determined as 120 cm(-)(1). Upon deprotonation, the IT band was not observed. It is therefore concluded that a superexchange pathway occurs predominantly via the Ru(II) dpi-bbbpyH(2) pi interaction, since deprotonation decreases the interaction. The role of the intervening fragments in the bridging ligand is discussed from the viewpoint of orbital energies and their orbital mixing with Ru dpi orbitals.

Journal Article↗
PubMed1977

Microscopy of the junctional region between human coronal primary and secondary dentine.

The juction between human primary dentine and regular and irregular secondary dentine was examined with a number of different light and electron microscopic techniques. In decalcified material, a narrow band along the innermost surface of the primary dentine stained intensely. The walls of the tubules within the band stained intensely, whereas the tubular walls within the bulk of the primary dentine were not stained. Generally, the walls of the tubules in both types of secondary dentine were also preferentially stained. Although not readily apparent in ground sections, observations of thin sections revealed a dramatic reduction in the number of tubules in regular secondary dentine. Generally, the radiodensity of the intertubular matrix was the same in primary and secondary dentine and the intensely stained band was not seen radiographically. The pulpal ends of the tubules in primary dentine were often occluded with a material having the same radiodensity as peritubular matrix. Both patent and occluded tubules were seen in irregular secondary dentine. Scanning electron microscopy of acid-etched specimens of secondary dentine revealed that some tubules had irregular walls of highly mineralized matrix which was less acid-soluble then the peritubular matrix of primary dentine.

Cuspid↗
PubMed1967

Ascorbic acid deficiency in cultured human fibroblasts.

Fibroblasts grown in medium containing less than 1 microg of ascorbic acid per milliliter showed evidence of ascorbic acid deficiency when compared with cells grown in medium containing 50 microg of ascorbic acid per milliliter. This was manifested morphologically by dilated endoplasmic reticulum, a decrease in number, size, and intensity of staining of the mitochondria, by defective intercellular fibril formation, and by easy disaggregation of the cells from the intercellular matrix after treatment with pronase. When 50 microg per milliliter of ascorbic acid was incorporated into the medium, the altered morphology was corrected, banded fibrils were produced which were organized into bundles, and the cells were tightly bound in a matrix which was resistant to disaggregation with a variety of proteolytic enzymes. Collagen and sulfated glycosaminoglycan synthesis were less in the control than in the ascorbic acid supplemented cells. Similar morphological and chemical changes have been reported in the connective tissue of scorbutic animals. The effects of low ascorbic acid concentration on fibroblasts in culture indicate that these cells require ascorbic acid to maintain connective tissue functions.

Amino Sugars↗