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At least 703 records · Page 39Linked to original sources
PubMed2003

Rapid LC-TOFMS method for identification of binding sites of covalent acylglucuronide-albumin complexes.

A method for rapid identification of binding sites of covalent adducts was developed using delta bilirubin as a model compound. Delta bilirubin, containing intact human serum albumin (HSA), was digested with trypsin and the peptide fragments were monitored at 436 nm, but no predominant peaks were detected indicating the instability of the digested peptides containing bilirubin-related compounds. Therefore, the high-performance liquid chromatography time-of-flight mass spectrometer (LC-TOFMS) data of digested fragments of delta bilirubin were compared with those of control digests of HSA, revealing a characteristic peptide in the digest mixture of delta bilirubin. This peptide was sequenced by high-performance liquid chromatography time-of-flight tandem mass spectrometry (LC-TOFMS/MS) and identified as LDELRDEGKASSAK (Leu182 to Lys195) with a modification of a 178 Da increase at Lys190. This indicated the Lys190 to be a predominant covalent binding site of BGs on HSA via the imine mechanism and the binding between the bilirubin moiety and the glucuronic acid moiety to be unstable to digestion with trypsin. The method of comparing LC-TOFMS data requires no specific detection such as fluorescence or radioactivity for every compound. This should accelerate the structure elucidation of covalent adducts and be helpful for studying the relationship between the structure of ligands and specific binding sites.

Animals↗
PubMed2005

Genomic affinities in Arachis section Arachis (Fabaceae): molecular and cytogenetic evidence.

Section Arachis is the largest of nine sections in the genus Arachis and includes domesticated peanut, A. hypogaea L. Most species are diploids (x = 10) with two tetraploids and a few aneuploids. Three genome types have been recognized in this section (A, B and D), but the genomes are not well characterized and relationships of several newly described species are uncertain. To clarify genomic relationships in section Arachis, cytogenetic information and molecular data from amplified fragment length polymorphism (AFLP) and the trnT-F plastid region were used to provide an additional insight into genome composition and species relationships. Cytogenetic information supports earlier observations on genome types of A. cruziana, A. herzogii, A. kempff-mercadoi and A. kuhlmannii but was inconclusive about the genome composition of A. benensis, A. hoehnei, A. ipaensis, A. palustris, A. praecox and A. williamsii. An AFLP dendrogram resolved species into four major clusters and showed A. hypogaea grouping closely with A. ipaensis and A. williamsii. Sequence data of the trnT-F region provided genome-specific information and showed for the first time that the B and D genomes are more closely related to each other than to the A genome. Integration of information from cytogenetics and biparentally and maternally inherited genomic regions show promise in understanding genome types and relationships in Arachis.

Arachis↗
PubMed1997

Phylogenetic analyses of DNA and allozyme data suggest that Gonioctena leaf beetles (Coleoptera; Chrysomelidae) experienced convergent evolution in their history of host-plant family shifts.

A phylogenetic analysis of the genus Gonioctena (Coleoptera, Chrysomelidae) based on allozyme data (17 loci) and mitochondrial DNA sequence data (three gene fragments, 1,391 sites) was performed to study the evolutionary history of host-plant shifts among these leaf beetles. This chrysomelid genus is characteristically associated with a high number of different plant families. The diverse molecular data gathered in this study are to a large extent congruent, and the analyses provide a well-supported phylogenetic hypothesis to address questions about the evolution of host-plant shifts in the genus Gonioctena. The most-parsimonious reconstruction of the ancestral host-plant associations, based on the estimated phylogeny, suggests that the Fabaceae was the ancestral host-plant family of the genus. Although most of the host-plant shifts (between different host species) in Gonioctena have occurred within the same plant family or within the same plant genus, at least eight shifts have occurred between hosts belonging to distantly related and chemically dissimilar plant families. In these cases, host shifts may have been simply directed toward plant species available in the environment. Yet, given that two Gonioctena lineages have independently colonized the same three new plant families (Salicaceae, Betulaceae, Rosaceae), including four of the same new genera (Salix, Alnus, Prunus, Sorbus), some constraints are likely to have limited the different possibilities of interfamilial host-plant shifts.

Animals↗
PubMed2001

Increase of fat oxidation and weight loss in obese mice caused by chronic treatment with human growth hormone or a modified C-terminal fragment.

OBJECTIVE: To observe the chronic effects of human growth hormone (hGH) and AOD9604 (a C-terminal fragment of hGH) on body weight, energy balance, and substrate oxidation rates in obese (ob/ob) and lean C57BL/6Jmice. In vitro assays were used to confirm whether the effects of AOD9604 are mediated through the hGH receptor, and if this peptide is capable of cell proliferation via the hGH receptor. METHOD: Obese and lean mice were treated with hGH, AOD or saline for 14 days using mini-osmotic pumps. Body weight, caloric intake, resting energy expenditure, fat oxidation, glucose oxidation, and plasma glucose, insulin and glycerol were measured before and after treatment. BaF-BO3 cells transfected with the hGH receptor were used to measure in vitro 125I-hGH receptor binding and cell proliferation. RESULTS: Both hGH and AOD significantly reduced body weight gain in obese mice. This was associated with increased in vivo fat oxidation and increased plasma glycerol levels (an index of lipolysis). Unlike hGH, however, AOD9604 did not induce hyperglycaemia or reduce insulin secretion. AOD9604 does not compete for the hGH receptor and nor does it induce cell proliferation, unlike hGH. CONCLUSIONS: Both hGH and its C-terminal fragment reduce body weight gain, increase fat oxidation, and stimulate lipolysis in obese mice, yet AOD9604 does not interact with the hGH receptor. Thus, the concept of hGH behaving as a pro-hormone is further confirmed. This data shows that fragments of hGH can act in a manner novel to traditional hGH-stimulated pathways.

Adipose Tissue↗
PubMed1997

An N-terminal fragment of titin coupled to green fluorescent protein localizes to the Z-bands in living muscle cells: overexpression leads to myofibril disassembly.

Cultures of nonmuscle cells, skeletal myotubes, and cardiomyocytes were transfected with a fusion construct (Z1.1GFP) consisting of a 1.1-kb cDNA (Z1.1) fragment from the Z-band region of titin linked to the cDNA for green fluorescent protein (GFP). The Z1.1 cDNA encodes only 362 amino acids of the approximately 2000 amino acids that make up the Z-band region of titin; nevertheless, the Z1.1GFP fusion protein targets the alpha-actinin-rich Z-bands of contracting myofibrils in vivo. This fluorescent fusion protein also localizes in the nascent and premyofibrils at the edges of spreading cardiomyocytes. Similarly, in transfected nonmuscle cells, the Z1.1GFP fusion protein localizes to the alpha-actinin-containing dense bodies of the stress fibers in vivo. A dominant negative phenotype was also observed in living cells expressing high levels of this Z1.1GFP fusion protein, with myofibril disassembly occurring as titin-GFP fragments accumulated. These data indicate that the Z-band region of titin plays an important role in maintaining and organizing the structure of the myofibril. The Z1.1 cDNA was derived from a chicken cardiac lambda gt11 expression library, screened with a zeugmatin antibody. Recent work has suggested that zeugmatin is actually part of the N-terminal region of the 81-kb titin cDNA. A reverse transcriptase polymerase chain reaction using a primer from the distal end (5' end) of the Z1.1 zeugmatin cDNA and a primer from the nearest known proximal (3' end) chicken titin (also called connectin) cDNA resulted in a predicted 0.3-kb polymerase chain reaction product linking the two known chicken titin cDNAs to each other. The linking region had a 79% identity at the amino acid level to human cardiac titin. This result and a Southern blot analysis of chicken genomic DNA hybridized with Z1.1 add further support to our original suggestion that zeugmatin is a proteolytic fragment from the N-terminal region of titin.

Amino Acid Sequence↗
PubMed1989

The properties of retrieval cues constrain the picture superiority effect.

In three experiments, we examined why pictures are remembered better than words on explicit memory tests like recall and recognition, whereas words produce more priming than pictures on some implicit tests, such as word-fragment and word-stem completion (e.g., completing -l-ph-nt or ele----- as elephant). One possibility is that pictures are always more accessible than words if subjects are given explicit retrieval instructions. An alternative possibility is that the properties of the retrieval cues themselves constrain the retrieval processes engaged; word fragments might induce data-driven (perceptually based) retrieval, which favors words regardless of the retrieval instructions. Experiment 1 demonstrated that words were remembered better than pictures on both the word-fragment and word-stem completion tasks under both implicit and explicit retrieval conditions. In Experiment 2, pictures were recalled better than words with semantically related extralist cues. In Experiment 3, when semantic cues were combined with word fragments, pictures and words were recalled equally well under explicit retrieval conditions, but words were superior to pictures under implicit instructions. Thus, the inherently data-limited properties of fragmented words limit their use in accessing conceptual codes. Overall, the results indicate that retrieval operations are largely determined by properties of the retrieval cues under both implicit and explicit retrieval conditions.

Adult↗
PubMed1984

The immunoglobulin heavy chain variable region (Igh-V) locus in the mouse. I. One hundred Igh-V genes comprise seven families of homologous genes.

Seven families of Igh-V genes have been defined by Southern blot analysis of genomic DNA from eighteen inbred strains of mice. Each of twenty-four cloned Vh genes hybridized to one of seven nonoverlapping sets of Eco RI restriction fragments. These families contain from 2 to approximately 40 hybridizing fragments. From these data we estimate that the mouse Igh-V locus consists of one hundred Vh genes. Genes within a Vh family share greater than 80% sequence homology while the sequence homology between families is generally less than 70%. There is extensive restriction fragment length polymorphism among the strains analyzed allowing the assignment of complete (Igh-V + Igh-C) Igh haplotypes for eighteen inbred mouse strains.

Animals↗
PubMed2005

Optimization of cDNA-AFLP experiments using genomic sequence data.

MOTIVATION: cDNA amplified fragment length polymorphism (cDNA-AFLP) is one of the few genome-wide level expression profiling methods capable of finding genes that have not yet been cloned or even predicted from sequence but have interesting expression patterns under the studied conditions. In cDNA-AFLP, a complex cDNA mixture is divided into small subsets using restriction enzymes and selective PCR. A large cDNA-AFLP experiment can require a substantial amount of resources, such as hundreds of PCR amplifications and gel electrophoresis runs, followed by manual cutting of a large number of bands from the gels. Our aim was to test whether this workload can be reduced by rational design of the experiment. RESULTS: We used the available genomic sequence information to optimize cDNA-AFLP experiments beforehand so that as many transcripts as possible could be profiled with a given amount of resources. Optimization of the selection of both restriction enzymes and selective primers for cDNA-AFLP experiments has not been performed previously. The in silico tests performed suggest that substantial amounts of resources can be saved by the optimization of cDNA-AFLP experiments.

Algorithms↗
PubMed2007

Fragmentation of leucine enkephalin as a function of laser fluence in a MALDI TOF-TOF.

The effects of laser fluence on ion formation in MALDI were studied using a tandem TOF mass spectrometer with a Nd-YAG laser and alpha-cyano hydrocinnamic acid matrix. Leucine enkephalin ionization and fragmentation were followed as a function of laser fluence ranging from the threshold of ion formation to the maximum available, that is, about 280-930 mJ/mm2. The most notable finding was the appearance of immonium ions at fluence values close to threshold, increasing rapidly and then tapering in intensity with the appearance of typical backbone fragment ions. The data suggest the presence of two distinct environments for ion formation. One is associated with molecular desorption at low values of laser fluence that leads to extensive immonium ion formation. The second becomes dominant at higher fluences, is associated initially with backbone type fragments, but, at the highest values of fluence, progresses to immonium fragments. This second environment is suggestive of ion desorption from large pieces of material ablated from the surface. Arrhenius rate law considerations were used to estimate temperatures associated with the onset of these two processes.

Enkephalin, Leucine↗
PubMed1992

Cloning and mapping of EcoRI, HindIII, and PstI fragments of bovine herpesvirus 4 (DN-599) genome.

EcoRI, HindIII, and PstI restriction fragments representing the entire genome of the DN-599 isolate, the American prototype strain, of bovine herpesvirus 4 (BHV-4) were cloned. These cloned restriction fragments were analyzed by restriction enzyme digestion, hybridization to Southern blots of BHV-4 (DN-599) DNA, and cross-hybridization of cloned fragments. The resulting data were used to construct restriction maps of the unique region of BHV-4 (DN-599) DNA for restriction enzymes EcoRI, HindIII, and PstI. The EcoRI and HindIII restriction maps confirm those previously deduced for the DN-599 isolate by hybridization of cloned fragments of a European strain of BHV-4 to Southern blots of DN-599 DNA. The PstI restriction map is the first reported for BHV-4.

Animals↗
PubMed1985

GAWK, a novel human pituitary polypeptide: isolation, immunocytochemical localization and complete amino acid sequence.

During the course of reverse-phase high pressure liquid chromatography (RP-HPLC) purification of a postulated big ACTH (1) from human pituitary gland extracts, a highly purified peptide bearing no resemblance to any known polypeptide was isolated. The complete sequence of this 74 amino acid polypeptide, called GAWK, has been determined. Search on a computer data bank on the possible homology to any known protein or fragment, using a mutation data matrix, failed to reveal any homology greater than 30%. An antibody produced against a synthetic fragment allowed us to detect several immunoreactive forms. The antisera also enabled us to localize the polypeptide, by immunocytochemistry, in the anterior lobe of the pituitary gland.

Amino Acid Sequence↗
PubMed2001

Effect of bilirubin on lipid peroxidation, sphingomyelinase activity, and apoptosis induced by sphingosine and UV irradiation.

The effect of bilirubin (BR) on sphingomyelin cycle activity, lipid peroxidation (LPO), and apoptosis induced by sphingosine and UV irradiation has been studied in vivo. Neutral Mg(2+)-dependent sphingomyelinase (SMase) activity and LPO level were monitored in heart, kidney, and liver of mice after administration of BR. BR inhibited both LPO and SMase activities in heart and kidney. BR induced a mild increase in LPO level and moderate increase in lipid contents in liver, consistent with the functional role of liver in both BR and lipid metabolism. BR injected to mice causes simultaneous and unidirectional alterations in both LPO level and SMase activity with a significant (p < 0.05) positive linear correlation between these two parameters. Sphingosine administration results in increased lipid peroxidation in murine liver. Data on DNA fragmentation indicate that exogenous BR may effectively protect thymus cells against sphingosine- and UV-mediated apoptosis. These results have revealed a biochemical association between oxidative stress and BR on one hand and the sphingomyelin cycle and apoptotic cell death on the other hand. Our data show that BR as an antioxidant, due to its effect on the sphingomyelin cycle, can protect membrane lipids against peroxidation and cells against apoptosis induced by various factors.

Animals↗
PubMed2003

Inter-island movements and population differentiation in a pelagic seabird.

We used mark-resight data and amplified fragment length polymorphism (AFLP) markers to assess movements and gene flow between Central Pacific breeding colonies of the great frigatebird, Fregata minor. Of 715 adult frigatebirds marked on Tern Island and Johnston Atoll, 21.3% were resighted at other frigatebird colonies at least 582 km away. Mark-resight data indicated regular movement of males and females between Tern Island and Johnston Atoll (873 km apart), and less frequent movements to other islands; no birds marked on Tern or Johnston were seen on Christmas Island, but one was seen in the Philippines, 7627 km from where it was marked. Despite the regular occurrence of interisland movements, Bayesian analyses of AFLP data showed significant genetic differentiation between Tern Island and Johnston Atoll, and more pronounced differentiation between these two islands and the more distant Christmas Island. The AFLP profiles of three birds breeding on Tern Island fell within the profile-cluster typical for Christmas Island birds, both in a nonmetric multidimensional scaling analysis and in a population assignment test, suggesting dispersal events from Christmas Island to Tern Island. Several factors could explain the persistence of genetic structure despite frequent movements between colonies: many movements occurred during the nonbreeding season, many breeding-season movements did not involve mate-acquisition behaviours and individuals that do disperse may be selected against, as suggested by morphometric differences between colonies. The persistence of genetic structure among breeding colonies despite significant interisland movements suggests limits to the effectiveness of migration as a homogenizing force in this broadly distributed, extremely mobile species.

Animal Migration↗
PubMed1996

Calcium modulates plasmin cleavage of the fibrinogen D fragment gamma chain N-terminus: mapping of monoclonal antibody J88B to a plasmin sensitive domain of the gamma chain.

Plasmin sensitive sites are found on the A alpha, B beta and gamma chains of fibrinogen at regions joining the two C-terminal D fragments with the central E fragment. We have developed a monoclonal antibody (MoAb) reactive with this plasmin sensitive region on the human fibrinogen gamma chain and mapped its epitope. MoAb J88B reacts with gamma chains of both native as well as with reduced and denatured fibrinogen and fibrin, the CNBr fragment of the fibrinogen central domain, plasmin cleaved fragments D, gamma-gamma dimers, but not with plasmic fragments E. These data indicate that J88B maps to the plasmin sensitive domain localized to gamma 63-78. MoAb J88B failed to react with synthetic peptide gamma 70-78, which suggests that the epitope includes the newly exposed N-terminal residues gamma 63-70 of the early plasmic fragment D1A. As calcium has a marked influence on plasmin cleavage of C-terminal sites on the gamma chain, the effects of calcium on modulating plasmin cleavage of D1A to D1 were assessed in the absence or presence of J88B. The results indicated that calcium delays and J88B (+/- calcium) protects the gamma chain from plasmin cleavage at the N-terminus of D1A, suggesting that this enzymatically labile site is calcium-sensitive. Thus, MoAb J88B should prove useful in studies examining the structure of plasmin cleaved fibrinogen and fibrin.

Antibodies, Monoclonal↗
PubMed1997

Purification and characterization of a carboxylesterase associated with organophosphate resistance in the greenbug, Schizaphis graminum (Homoptera: Aphididae).

The Type II esterase associated with organophosphate resistance in the greenbug, Schizaphis graminum, was purified by column chromatography and preparative electrophoresis resulting in over 100-fold purification and approximately 11% recovery. The native enzyme appears to exist as a heterodimer with the subunits equal to 52 and 56 kDa. The mass of the native enzyme was estimated at 102 kDa by gel filtration chromatography and the isoelectric focusing point was 4.8. The enzyme was inhibited by both paraoxon and mercuric chloride, suggesting that it is a serine hydrolase, although it was not inhibited by carbamate insecticides or eserine. The enzyme was active toward both beta- and alpha-naphthol esters, although the length of the side chain (C-2 or C-4) also affected activity. The enzyme displayed no activity toward acetylthiocholine. N-Terminal amino acid sequence analysis of the enzyme subunits indicates that residues Val-4 and Gly-10 of the larger fragment were highly conserved among 11 other carboxylesterase sequences. Sequence data from the smaller fragment did not reveal any similarity with other esterase sequences.

Amino Acid Sequence↗
PubMed1987

Meiotic non-disjunction induced by fission neutrons relative to X-rays observed in mouse secondary spermatocytes. II. Dose-effect relationships after treatment of pachytene cells.

(C57B1/Cne X C3H/Cne)F1 male mice were irradiated with single acute doses of 0.4 MeV neutrons (from 0.11 to 0.72 Gy) or 250 kV X-rays (from 0.25 to 3 Gy) and sacrificed 5 days later. Chromosome preparations of secondary spermatocytes, irradiated at the stage of pachytene, were analysed and the incidence of hyper-haploidies and chromosome fragments was recorded. Data on numerical aberrations were fitted by highly significant linear relationships for both types of radiation. A relative biological effectiveness (RBE) value of 5.65 was estimated by the ratio between the slopes of the two regression lines. The same linear fitting was applied to frequencies of cells with fragments, even if in this case other types of functions could not be excluded. An RBE value was estimated in the same way as for numerical aberrations and yielded a comparable figure of 5.23. A significant correlation was also found between the incidence of numerical and structural aberrations, which points to the chromosome itself as the prevalent target for radiation-induced non-disjunction (ND). In addition, the highly significant linearity of the dose-effect relationship observed for the induction of aneuploidies suggests, as the simplest hypothesis, a single-hit mechanism of radiation action, possibly through pre-non-disjunctional damage to the centromeric region, rather than an indirect induction of segregational difficulties after primarily induced chromatid interchanges.

Aneuploidy↗
PubMed2001

Nucleotide diversity in populations of balitorid cave fishes from Thailand.

Genetic variabilities in four cave and eight surface species of balitorid freshwater fishes from Thailand were assessed using random amplified polymorphic DNA (RAPD). Cave species have consistently lower RAPD variation than surface species and it is hypothesized that this difference is a function of reduced population size in cave fishes. Indices of nucleotide diversity (pi) were calculated from the RAPD data and are four to five times higher for the surface species than the cave species: 6.4 x 10-3 vs. 1.4 x 10-3. The pi-values for cave fishes are significantly lower than those for surface balitorids and those measured in other species using RAPD/amplified fragment length polymorphism data.

Animals↗