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At least 829 records · Page 46Linked to original sources
PubMed1998

Stimulation of inducible nitric oxide synthase in rat liver by hyaluronan fragments.

Hepatic injury and chronic wounding are characterized by increased synthesis of extracellular matrix proteins including hyaluronan (HA). Recently, it has been recognized that low-molecular-weight fragments of HA, but not native HA (e.g., high-molecular-weight HA), induce inflammatory gene expression, and activate the transcriptional regulator, nuclear factor kappaB (NF-kappaB). The inducible isoform of nitric oxide synthase (iNOS) is induced by cytokines and/or lipopolysaccharide (LPS) through the NF-kappaB signal transduction pathway. Because of this association, we hypothesized that HA fragments might also stimulate iNOS gene transcription. The aims of this study were therefore to determine whether HA or HA fragments induced iNOS in hepatic cells, and to characterize the signaling pathway. HA fragments (100 microg/mL) markedly stimulated iNOS messenger RNA (mRNA) in endothelial and Kupffer cells, but minimally induced this mRNA in hepatocytes and stellate cells. High-molecular-weight HA (200 microg/mL) had no effect on iNOS mRNA in any cell type. The addition of interferon gamma (IFN-gamma) to HA fragments resulted in stimulation of iNOS mRNA 2-, 3-, 4-, and 10-fold above that for HA fragments alone in hepatocytes, endothelial, Kupffer, and stellate cells, respectively. The combination of HA fragments and LPS did not result in an incremental increase in iNOS mRNA induction. iNOS protein and nitrite levels (used as a measure of NO production and NOS enzymatic activity) paralleled closely iNOS mRNA expression and increased proportionally to HA fragment concentration in a dose-dependent fashion. At 1 hour following stimulation, NF-kappaB DNA binding activity was detected in extracts from Kupffer cells stimulated with HA fragments, but not in those exposed to media alone or to high-molecular-weight HA. Finally, inhibitors of NF-kappaB blocked HA fragment-dependent iNOS mRNA induction in Kupffer and sinusoidal endothelial cells. The data indicate that HA fragments, but not high-molecular-weight HA, induce iNOS in liver, having the greatest effects on endothelial and Kupffer cells. We speculate that HA fragments may be an important stimulus for NO production in various forms of liver disease, particularly as a cofactor with inflammatory cytokines.

Animals↗
PubMed1993

Mannose-specific lectins bind alpha-2-macroglobulin and an unknown protein from human plasma.

GNA, the mannose-specific lectin from Galanthus nivalis was confirmed to bind alpha-2-macroglobulin (A2M) but another protein was copurified with A2M from total human plasma. A total of 23 other lectins with diverse specificities were tested for reaction with human A2M and with three other members of the A2M family. NPA, a mannose-specific lectin isolated from Narcissus pseudonarcissus bulbs, and RSA, the Rhizoctonia solani agglutinin, were selected for further testing. For isolation of A2M, immobilized NPA was superior to GNA because its binding capacity was an order of magnitude higher. The specificity of these lectins must be very similar however, because the same unknown plasma protein was also bound by NPA. A2M and the unknown protein must share a unique mannose carbohydrate structure not present in any other human plasma protein. The copurified protein subunit size of 185 kDa is very similar to that of A2M, but the native molecular mass of 350 kDa indicated a noncovalent homodimer structure. Together with the acid isoelectric point this is not typical for any known plasma protein nor for any unidentified spot on the two-dimensional map of human plasma proteins. No immunological reaction with available antisera was evident. A specific antiserum raised to the unknown protein demonstrated its presence in all human plasma samples examined. The N-terminal residue was blocked, whereas internal protein sequences obtained after CNBr fragmentation and proteolysis were not homologous to any known protein sequence. These data demonstrate that this protein is unknown and not a proteinase inhibitor of the A2M family.

Amino Acid Sequence↗
PubMed2005

Progress in computation and amide hydrogen exchange for prediction of protein-protein complexes.

The macromolecular docking problem that must be solved for experimental biologists is prediction of the structures of complexes for which the components are known or reliably modeled in the unbound state, but the structure of the complex is unknown. The current state of the art in macromolecular docking is such that solving this problem usually requires supplementary experimental chemical and/or biological information to evaluate computational predictions. Amide (1)H/(2)H exchange measured by mass spectroscopy is a promising approach for obtaining such information, because it can reveal interfacial regions of each member of the complex and identify regions of conformational flexibility in the structure. In a previous article (Anand et al., Proc Natl Acad Sci USA 2003;100:13264-13269), we used (1)H/(2)H exchange data to predict the structure of a complex between regulatory and catalytic subunits of protein kinase A. Comparison of the prediction with a recent crystal structure determination (Kim et al., Science 2005;307:690-696) showed large conformational change in the regulatory subunit on formation of the complex. Analysis of the prediction, previous CAPRI results, novel data processing methods for the (1)H/(2)H exchange data, and new fragment docking computations give grounds for cautious optimism that this method can be useful even in cases of substantial conformational change.

Algorithms↗
PubMed2005

Electrospray ionization mass spectrometry for identification and structural characterization of pregnane glycosides.

Pregnane glycosides are a class of naturally occurring substances characterized by some interesting biological activities and widely distributed in the plant kingdom and in some marine organisms. Their toxicity and use in herbal drugs and folk medicines has generated great interest in the chemical characterization of these molecules. In the study reported here the potential of electrospray ionization mass spectrometry (ESI-MS) in the identification and structural characterization of pregnane glycosides was examined. ESI-MS/MS and ESI-MS(n) analyses were performed on 27 different compounds employing two mass spectrometers equipped with a triple-quadrupole or an ion-trap analyzer. The data illustrate the ability of the ESI techniques in the identification of pregnane glycosides, including the nature of the pregnane core, the kind of ester substituents, the types of sugar residues (hexose, deoxyhexose, dideoxyhexose, O-methyldeoxyhexose and O-methyldideoxyhexose), and the primary structure of the saccharide chain. From these data, a generalized fragmentation pathway was proposed by comparing the spectra acquired for all the compounds. Interestingly, similar results were obtained from the two instruments, thus demonstrating that detailed analyses of product ion spectra obtained using a triple-quadrupole mass spectrometer led to structural information comparable to those obtainable in MSn experiments using an ion trap. Different and complementary information was deduced by fragmenting the [M+H]+ or the [M+Na]+ ions, or the protonated aglycone [Agl+H]+ generated by in-source fragmentation. The present evidence clearly suggests that, in order to obtain a complete characterization of pregnane glycosides by MS, all three of these species should be accurately analyzed.

Apocynaceae↗
PubMed2001

Study of the electrospray ionization mass spectrometry of the proton pump inhibiting drug Omeprazole.

A detailed analysis of the product ion spectrum generated from the protonated molecule under ESI-MS/MS conditions using a triple quadrupole mass spectrometer is reported for the gastrointestinal proton pump inhibitor Omeprazole. Unambiguous molecular composition data of the fragment ions were obtained with the aid of regioselectively 14C-, 34S- and 18O-labeled analogs. Attempts have been made to provide rational pathways for the formation of the fragment ions from four protonated omeprazole species. These results will facilitate the characterization of the complex metabolic fate of Omeprazole in humans, which involves the excretion of at least 50 metabolites.

Carbon Radioisotopes↗
PubMed2002

Study of the electrospray ionization tandem mass spectrometry of sildenafil derivatives.

A detailed analysis of the product ion spectrum generated from the protonated molecule of sildenafil (Viagra(R)) under multiple tandem mass spectrometry (ESI-MS(n)) conditions using an ion-trap mass spectrometer is reported. Molecular composition data of the fragment ions were obtained with the aid of comparisons of the multiple tandem mass spectra of eight sildenafil derivatives in two series, the structures of which are identical except for some substituted alkyl groups. Attempts have been made to provide rational pathways for the formation of the fragment ions from these protonated sildenafil derivatives. The structure-fragmentation relationships will facilitate the characterization of the structures of other sildenafil analogs.

Piperazines↗
PubMed1997

Physical mapping of potassium channel gene clusters on mouse chromosomes three and six.

Mammalian voltage-gated K channel genes have been divided into four subfamilies (Shaker, Shab, Shal, and Shaw) based on their sequence identity and similarity to related genes in Drosophila. Genetic mapping of the voltage-gated K channel genes has shown that similar multigene clusters exist on mouse Chr 3 and 6 and suggests that the clusters may have arisen through chromosomal duplication. In this report, YAC-based physical maps of the clustered mouse Shaker-like K channel genes have been constructed using restriction endonuclease and yeast chromosome fragmentation approaches. These data define the physical spacing as 5'-Kcna3-(60 kb)-Kcna2-(90 kb)-Kcna8-3' on Chr 3, and as 5'-Kcna6-(80 kb)-Kcna1-(110 kb)-Kcna5-3' on Chr 6, with all genes oriented in a head-to-tail manner within their respective clusters. These detailed physical maps of both K channel gene clusters provide additional support for the idea of an ancient genome tetraploidization event.

Animals↗
PubMed1999

Antibody binding defines a structure for an epitope that participates in the PrPC-->PrPSc conformational change.

The X-ray crystallographic structures of the anti-Syrian hamster prion protein (SHaPrP) monoclonal Fab 3F4 alone, as well as the complex with its cognate peptide epitope (SHaPrP 104-113), have been determined to atomic resolution. The conformation of the decapeptide is an Omega-loop. There are substantial alterations in the antibody combining region upon epitope binding. The peptide binds in a U-shaped groove on the Fab surface, with the two specificity determinants, Met109 and Met112, penetrating deeply into separate hydrophobic cavities formed by the heavy and light chain complementarity-determining regions. In addition to the numerous contacts between the Fab and the peptide, two intrapeptide hydrogen bonds are observed, perhaps indicating the structure bound to the Fab exists transiently in solution. This provides the first structural information on a portion of the PrP N-terminal region observed to be flexible in the NMR studies of SHPrP 90-231, SHaPrP 29-231 and mouse PrP 23-231. Antibody characterization of the antigenic surfaces of PrPC and PrPSc identifies this flexible region as a component of the conformational rearrangement that is an essential feature of prion disease.

Animals↗
PubMed1999

C-H.O hydrogen bonds in minor groove of A-tracts in DNA double helices.

Analysis of available B-DNA type oligomeric crystal structures as well as protein-bound DNA fragments (solved using data with resolution <2.6 A) indicates that in both data sets, a majority of the (3'-Ade) H2..O2(3'-Thy/Cyt) distances in AA.TT and GA.TC dinucleotide steps, are considerably shorter than their values in a uniform fibre model, and are smaller than their optimum separation distance. Since the electropositive C2-H2 group of adenine is in close proximity of the electronegative keto oxygen atoms of both pyrimidine bases in the antiparallel strand of the double-helical DNA structures, it suggests the possibility of intra-base-pair as well as cross-strand C-H..O hydrogen bonds in the minor groove. The C2-H2..O2 hydrogen bonds within the A.T base-pairs could be a natural consequence of Watson-Crick pairing. However, the close cross-strand interactions between the bases at the 3'-ends of the AA.TT and GA.TC steps arise due to the local sequence-dependent geometry of these steps. While the base-pair propeller twist in these steps is comparable to the fibre model, some of the other local parameters such as base-pair opening angle and inter-base-pair slide show coordinated changes, leading to these shorter C2-H2..O2 distances. Hence, in addition to the well-known minor groove hydration, it appears that favourable C2-H2..O2 cross-strand interactions may play a role in imparting a characteristic geometry to AA.TT and GA.TC steps, as well as An.Tn and GAn.TnC tracts, which leads to a narrow minor groove in these regions.

Base Pairing↗
PubMed1999

Reevaluation of phylogeny in the Drosophila obscura species group based on combined analysis of nucleotide sequences.

The Drosophila obscura species group has served as an important model system in many evolutionary and population genetic studies. Despite the amount of study this group has received, some phylogenetic relationships remain unclear. While individual analysis of different nuclear, mitochondrial, allozyme, restriction fragment, and morphological data partitions are able to discern relationships among closely related species, they are unable to resolve relationships among the five obscura species subgroups. A combined analysis of several nucleotide data sets is able to provide resolution and support for some nodes not seen or well supported in analyses of individual loci. A phylogeny of the obscura species group based on combined analysis of nucleotide sequences from six mitochondrial and five nuclear loci is presented here. The results of several different combined analyses indicate that the Old World obscura and subobscura subgroups form a monophyletic clade, although they are unable to resolve the relationships among the major lineages within the obscura species group.

Animals↗
PubMed2003

Monitoring of a new approach of immunotherapy with allogenic (111)In-labelled NK cells in patients with renal cell carcinoma.

The transfusion of allogenic, in vitro expanded natural killer cells (NKC) is a novel therapy option in oncology. To date, however, the biodistribution and kinetics of allogenic NKC have not been investigated. Therefore, in this study three patients with renal cell carcinoma received 3-7 x 10(8) NKC labelled with indium-111 oxine with a tenfold excess of unlabelled cells during NKC therapy. Whole-body scintigrams were obtained (0.5-144 h) in the anterior and posterior views. Scintigrams were analysed using a region of interest technique, and single-photon emission tomography (SPET) studies of the abdomen were performed. Results were compared to those obtained with polymerase chain reaction (PCR) of the peripheral blood (determination of foreign DNA, nested PCR, limit of detection 0.01%). Shortly after transfusion of NKC, more than 50% of the activity was accumulated in the lungs. We observed redistribution effects from lungs to liver, spleen and bone marrow. No significant loss of activity could be detected. In two of four large metastases, tracer accumulation could be proven by SPET. As confirmed by scintigrams and PCR, the fraction of circulating transfused cells was low at all times. Long-term activity retention might be caused either by survival of the allogenic cells, as confirmed by PCR (up to 3 days p.i.), or by phagocytosis of labelled cellular fragments. However, PCR data and uptake in metastases indicated long survival of a portion of allogenic NKC. Such long survival and low retention of the cells in the lung are requirements for an effective immunotherapeutic approach.

Adult↗
PubMed2006

Lack of association between microsatellite instability and benign adrenal tumors.

BACKGROUND: The adrenal gland may give rise to pheochromocytomas, which are catecholamine-producing tumors originating from the adrenal medulla, or to adrenocortical tumors, which derive from the adrenocortical cortex and may be secreting or not. The genetic mechanisms underlying the formation of these tumors include somatic mutations in susceptibility genes, especially in the familial forms, and allelic loss, especially in chromosome 1. AIM: The aim of this study was to investigate a third genetic mechanism by evaluating microsatellite instability using the reference markers (Bat25, Bat26, D2S123, D5S346, D17S250) validated by the National Cancer Institute. Microsatellite loci were analyzed in 32 benign tumors, including 11 pheochromocytomas and 21 adrenocortical tumors, in patients with and without familial syndrome. RESULTS: The different alleles of microsatellite loci were reliably detected by DNA fragments analysis, whereas data obtained after melting-point analysis on the Lightcycler were inconsistent. No microsatellite instability was detected in any tumor. One patient with a unilateral pheochromocytoma showed a loss of heterozygosity for D17S250. A second patient with a MEN-2A syndrome and a two-sided pheochromocytoma exhibited a loss of heterozygosity for D2S123 in the right tumor only and a retention of heterozygosity for all markers in the left tumor. CONCLUSIONS: These results suggest that microsatellite instability, evaluated by the five reference markers of the National Cancer Institute, is not a feature of benign adrenal tumors.

Adrenal Gland Neoplasms↗
PubMed1998

Cognitive decline unlike normal aging is associated with alterations of EEG temporo-spatial characteristics.

The diagnosis of beginning dementia is based mainly on neuropsychological testing. Several measures of EEG spectral composition, coherence and complexity (correlation dimension) have been shown to correspond to cognitive function. Only a few studies have evaluated EEG changes in normal aging, and no quantitative study has addressed changes in EEG during cognitive tasks in demented elderly. In this study the quantitative descriptors of EEGs from 31 demented or cognitively impaired elderly persons, 30 healthy elderly (mean age 69 years) and 35 young controls (mean age 31 years) were compared. The EEGs were recorded during two resting conditions (eyes closed and eyes opened) and two tasks (mental arithmetics and a lexical decision). The goal of the study was to evaluate which temporal and spatial EEG descriptors change with cognitive decline and with normal aging, respectively. Cognitive categories (unimpaired, impaired, demented) were based on Structured Interview for the Diagnosis of Dementia of Alzheimer Type (SIDAM) scores. The EEGs were analysed using adaptive segmentation of continuous EEG, which quantifies the succession of distinct stable topographic voltage patterns (EEG microstates). The main findings were a significant increase in the number of ultra-short EEG microstates and, independently, a reduction in the average duration of EEG microstates in the cognitively impaired and demented patients. In addition, cognitive impairment was associated with a reduction or loss of EEG reactivity normally observed when the resting states with closed and with opened eyes are compared. No alterations in temporal or spatial EEG descriptors were found in normal aging. Cognitive tasks did not add to information already obtained during the resting states. The reduction in EEG microstate duration correlated with loss of cognitive function. Temporo-spatial analysis of EEG therefore is a useful indicator of cortical dysfunction in dementia, correlating with the degree of cognitive impairment. Normal aging seems not to be accompanied by changes in temporo-spatial EEG patterns. The data suggest that fragmentation of the electrophysiological processes underlies cognitive dysfunction in Alzheimer's disease.

Adult↗
PubMed2002

Mitochondrial DNA sequence variation suggests the lack of genetic heterogeneity in the Adriatic and Ionian stocks of Sardina pilchardus.

A genetic stock structure analysis of 11 sardine samples from the Adriatic Sea and Ionian neighboring area was carried out through sequence variation analysis of a 307-bp cytochrome b gene fragment in order to identify self-recruiting units in the Adriatic Sardina pilchardus stock. The overall lack of genetic subdivision among samples detected by analysis of molecular variance, pairwise Phi(st) values, and the exact test of population differentiation indicates this sardine stock is part of a larger self-recruiting population whose boundaries are larger than the investigated area. This conclusion is in agreement with preliminary allozymic and mitochondrial DNA restriction fragment length polymorphism data, but contradicts the previous identification of 2 subpopulations of sardines in the Adriatic Sea argued on morphologic differences, which could be rather attributed to different hydrographic or ecologic conditions occurring in different areas of the Adriatic Sea. The reduced gene flow observed between Adriatic-Ionian and Spanish sardine geographic samples (P < 0.001) suggests that reproductively isolated populations of sardines may occur in the Mediterranean Sea.

Journal Article↗
PubMed2003

Population structure and variation in red snapper (Lutjanus campechanus) from the Gulf of Mexico and Atlantic coast of Florida as determined from mitochondrial DNA control region sequence.

The mitochondrial DNA control regions of red snapper (Lutjanus campechanus) from the Gulf of Mexico (n = 140) and Atlantic coast of Florida (n = 35) were sequenced to generate a prestocking genetic baseline for planned stock enhancement. Intrasample haplotype and nucleotide diversities ranged from 0.94 to 1.00 and 1.8% to 2.5%, respectively. All population analyses were consistent with the hypothesis that red snapper constitute a single, panmictic population over the sampled range. A ubiquitous, predominant haplotype, shared by 23% of the specimens, appeared to be evolutionarily recent, in contrast to previous findings based on restriction fragment length polymorphism data. Tajima's D values were suggestive of a recent bottleneck. Mismatch distributions from Gulf samples were smooth and unimodal, characteristic of recent population expansion. However, the Atlantic sample exhibited a comparatively broader, possibly multimodal distribution, suggestive of a more stable population history. Additional control-region data may clarify potentially disparate demographic histories of Gulf and Atlantic snapper.

Animals↗
PubMed1985

Repair of psoralen and acetylaminofluorene DNA adducts by ABC excinuclease.

Escherichia coli UvrA, UvrB and UvrC proteins acting in concert remove the major ultraviolet light-induced photoproduct, the pyrimidine dimer, from DNA in the form of a 12 to 13-nucleotide long single-stranded fragment. In vivo data indicate that the UvrABC enzyme is also capable of removing other nucleotide diadducts as well as certain nucleotide monoadducts from DNA and initiating the repair process that leads to removal of interstrand crosslinks caused by some bifunctional chemical agents. We have determined the action mechanism of the enzyme on nucleotide monoadducts produced by 4'-hydroxymethyl-4,5',8-trimethylpsoralen and N-acetoxy-N-2-acetylaminofluorene. In both cases we find that the enzyme hydrolyzes the eighth phosphodiester bond 5' and the fifth phosphodiester bond 3' to the modified base. This cutting pattern is similar to that observed with diadduct substrate, the only difference being that while the enzyme incises the fourth or fifth phosphodiester bond 3' to the pyrimidine dimer it always hydrolyzes the fifth bond relative to monoadducts. Our results also suggest that ABC excinuclease cuts the same two phosphodiester bonds on both sides of a T whether that T has a psoralen monoadduct or is involved in psoralen-mediated interstrand crosslink.

2-Acetylaminofluorene↗
PubMed1992

Further analyses of the orthopoxviruses volepox virus and raccoon poxvirus.

Volepox virus (VPX) from skin lesions on a vole and a piñon mouse caught in California and raccoon poxvirus (RCN) from raccoons trapped in Maryland were examined to begin elucidating their relationship to other orthopoxviruses, most of which are not known to be indigenous to the Americas. VPX and RCN produced pinpoint, nonhemorrhagic pocks on chick embryo chorioallantoic membranes. In cell cultures both viruses produced 1-mm diameter, irregular plaques, A-type inclusions (ATIs), and despite production of hemagglutinin, both viruses caused syncytia formation. Considerable cross-hybridization was seen between VPX and RCN DNA and the DNAs of other orthopoxviruses; however, HindIII cleavage site maps showed marked central and terminal region differences between VPX (222.8 kbp) and RCN (224.8 kbp) DNA and mapped DNAs of other orthopoxviruses. Cognate DNAs of the ATI 160-kDa protein and 38-kDa serine protease inhibitor homologue of cowpox virus (CPV) and the 14-kDa fusion protein of vaccinia virus (VAC) were present within the right end of VPX and RCN DNA, matching their location in CPV and VAC. VPX and RCN, respectively, expressed a 150- and a 155-kDa ATI major protein and a 20- and an 18-kDa fusion protein. Low stringency annealing suggested that cognate DNAs for the VAC growth factor and the alpha-amanitin target protein were present within the left end of VPX and RCN DNA, matching their location in VAC. Terminal tandem repeat sequences of VAC and RCN did not cross-hybridize with each other or with VPX DNA end fragments. Together, the data suggested that VPX and RCN are phylogenetically rather distant from orthopoxviruses not indigenous to the Americas, although genetic information is arranged as in other examined orthopoxviruses.

Animals↗
PubMed1992

Characterization of a myosin heavy chain gene from Brugia malayi.

We have previously shown that an antigen recognized by antibodies in sera of several microfilaremic individuals from a Wuchereria bancrofti endemic area bears strong homology to an invertebrate muscle protein. We have cloned and sequenced the entire gene containing this antigen encoding fragment and present data that confirms that the antigen is myosin heavy chain (MHC). This gene, which we have named Bmmyo-1 extends over 11 kb and has the potential to encode a protein of 1957 amino acids. The coding sequence is interrupted by 14 introns, most of which are larger than those in the myosin gene of the free-living nematode, Caenorhabditis elegans. The protein encoded by this gene bears greatest homology (75.1% identity) to the C. elegans myosin isoform MHC-B, encoded by the unc-54 gene. MHC-B is the major body wall myosin in C. elegans.

Amino Acid Sequence↗