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At least 1,153 records · Page 64Linked to original sources
PubMed1996

Reversible photobleaching of fluorescein conjugates in air-saturated viscous solutions: singlet and triplet state quenching by tryptophan.

Fluorescence recovery after photobleaching (FRAP) measurements on air-saturated aqueous solutions of fluorescein made viscous with glycerol or sucrose revealed a rapid component of fluorescence recovery with exponential time constants of 30-120 microseconds at viscosities of 15-300 cP. The rapid recovery process was not related to fluorophore translational diffusion and was insensitive to fluorophore concentration and the additive used to increase solution viscosity. At constant viscosity, the rate of reversible photobleaching recovery increased 2.5-fold in an O2- vs N2-saturated solution. The relative efficiency of reversible-to-irreversible photobleaching decreased with increasing photobleaching time and/or beam intensity. Reversible photobleaching was also detected for conjugates of fluorescein with dextrans and proteins in viscous media. In screening triplet state quenchers that might influence the reversible recovery, it was found that tryptophan enhanced the rate of reversible photobleaching recovery (two-fold increase at 8 mM) and quenched the fluorescein singlet state (Stern-Volmer constant, 12 M-1). Analysis of fluorescein lifetimes and photobleaching parameters for a series of fluorescein-labeled proteins with different numbers of tryptophans were also carried out. The results provide evidence for an oxygen-dependent, reversible photobleaching mechanism for the fluorescein chromophore involving triplet state relaxation. The identification of reversible fluorescein photobleaching has important implications for FRAP measurements of rapid solute diffusion in biological systems.

Fluoresceins↗
PubMed2001

Recognition of hypermethylated triplet repeats in vitro by cationic nanoparticles.

Genomic DNA contains many higher-order structural deviations from the Watson-Crick global average. The massive expansion and hypermethylation of the duplex triplet repeat (CCG)(n)(CGG)(n) has characteristic higher-order structures that are associated with the fragile X syndrome. We have used luminescent mineral nanoparticles of protein-sized cadmium sulfide in optical assays to detect anomalous DNA structures. The photoluminescence of these particles is sensitive to the presence and nature of adsorbates. We previously found that our nanoparticles bind the fragile X repeat well but do not bind to normal double-helical DNA. In this study, we have determined that these particles are also able to detect the hypermethylated forms of these triplet repeats. Therefore, these nanoparticles may form the basis for future optical assays of higher-order DNA structures, especially those associated with human disease.

Base Sequence↗
PubMed1994

Preferential nucleosome assembly at DNA triplet repeats from the myotonic dystrophy gene.

The expansion of CTG repeats in DNA occurs in or near genes involved in several human diseases, including myotonic dystrophy and Huntington's disease. Nucleosomes, the basic structural element of chromosomes, consist of 146 base pairs of DNA coiled about an octamer of histone proteins and mediate general transcriptional repression. Electron microscopy was used to examine in vitro the nucleosome assembly of DNA containing repeating CTG triplets. The efficiency of nucleosome formation increased with expanded triplet blocks, suggesting that such blocks may repress transcription through the creation of stable nucleosomes.

DNA↗
PubMed1968

Nonsense suppression in a multiauxotrophic derivative of Escherichia coli 15T-: identification and consequences of an amber triplet in the deoxyribomutase gene.

Previously, arginine revertants of Escherichia coli WWU, a derivative of E. coli 15T(-), have been subdivided by two independent methods: (i) the streak morphology on nutrient agar, and (ii) the pattern of phage growth using amber and ochre mutants of bacteriophage T4. In the first assay, revertants were subdivided into two classes according to the appearance of streaks after incubation on nutrient agar, a thick, even line of growth defining normal revertants and a thin, irregular line defining aberrant revertants. In the second assay, revertants were classified by the suppressors they contained. The present work demonstrates that revertants containing an amber suppressor show the aberrant morphology and are also able to catabolize thymidine for energy and carbon. This is in contrast to the parent WWU containing no suppressor, which shows a normal morphology and cannot utilize thymidine as an energy source. Revertants containing no suppressor, isolated specifically for their ability to catabolize thymidine, show an aberrant morphology. Together, these results indicate that the aberrant morphology results from suppression of an amber triplet in a gene of the thymidine catabolic pathway. Enzyme assays show the amber triplet to be in the gene specifying deoxyribomutase. It is suggested that the aberrant arginine revertants are analogous to high thymine-requiring mutants and that, in general, high and low thymine-requiring mutants differ from one another in their ability to catabolize deoxyribose-1-phosphate.

Arginine↗
PubMed2000

Hepatitis C virus internal ribosome entry site (IRES) stem loop IIId contains a phylogenetically conserved GGG triplet essential for translation and IRES folding.

The hepatitis C virus (HCV) internal ribosome entry site (IRES) is a highly structured RNA element that directs cap-independent translation of the viral polyprotein. Morpholino antisense oligonucleotides directed towards stem loop IIId drastically reduced HCV IRES activity. Mutagenesis studies of this region showed that the GGG triplet (nucleotides 266 through 268) of the hexanucleotide apical loop of stem loop IIId is essential for IRES activity both in vitro and in vivo. Sequence comparison showed that apical loop nucleotides (UUGGGU) were absolutely conserved across HCV genotypes and the GGG triplet was strongly conserved among related Flavivirus and Pestivirus nontranslated regions. Chimeric IRES elements with IIId derived from GB virus B (GBV-B) in the context of the HCV IRES possess translational activity. Mutations within the IIId stem loop that abolish IRES activity also affect the RNA structure in RNase T(1)-probing studies, demonstrating the importance of correct RNA folding to IRES function.

5' Untranslated Regions↗
PubMed1999

Stability of the human fragile X (CGG)(n) triplet repeat array in Saccharomyces cerevisiae deficient in aspects of DNA metabolism.

Expanded trinucleotide repeats underlie a growing number of human diseases. The human FMR1 (CGG)(n) array can exhibit genetic instability characterized by progressive expansion over several generations leading to gene silencing and the development of the fragile X syndrome. While expansion is dependent upon the length of uninterrupted (CGG)(n), instability occurs in a limited germ line and early developmental window, suggesting that lineage-specific expression of other factors determines the cellular environment permissive for expansion. To identify these factors, we have established normal- and premutation-length human FMR1 (CGG)(n) arrays in the yeast Saccharomyces cerevisiae and assessed the frequency of length changes greater than 5 triplets in cells deficient in various DNA repair and replication functions. In contrast to previous studies with Escherichia coli, we observed a low frequency of orientation-dependent large expansions in arrays carrying long uninterrupted (CGG)(n) arrays in a wild-type background. This frequency was unaffected by deletion of several DNA mismatch repair genes or deletion of the EXO1 and DIN7 genes and was not enhanced through meiosis in a wild-type background. Array contraction occurred in an orientation-dependent manner in most mutant backgrounds, but loss of the Sgs1p resulted in a generalized increase in array stability in both orientations. In contrast, FMR1 arrays had a 10-fold-elevated frequency of expansion in a rad27 background, providing evidence for a role in lagging-strand Okazaki fragment processing in (CGG)(n) triplet repeat expansion.

14-3-3 Proteins↗
PubMed2006

Inferring phylogenetic relationships avoiding forbidden rooted triplets.

To construct a phylogenetic tree or phylogenetic network for describing the evolutionary history of a set of species is a well-studied problem in computational biology. One previously proposed method to infer a phylogenetic tree/network for a large set of species is by merging a collection of known smaller phylogenetic trees on overlapping sets of species so that no (or as little as possible) branching information is lost. However, little work has been done so far on inferring a phylogenetic tree/network from a specified set of trees when in addition, certain evolutionary relationships among the species are known to be highly unlikely. In this paper, we consider the problem of constructing a phylogenetic tree/network which is consistent with all of the rooted triplets in a given set C and none of the rooted triplets in another given set F. Although NP-hard in the general case, we provide some efficient exact and approximation algorithms for a number of biologically meaningful variants of the problem.

Algorithms↗
PubMed1991

Neuronal pair and triplet interactions in the auditory midbrain of the leopard frog.

1. With the use of two independent microelectrodes and multiunit spike separation, 26 neural pairs, 17 triplets, and 8 quadruplets were recorded in the auditory midbrain of the leopard frog, resulting in a total of 125 neural pairs. 2. Functional interrelationships between neurons were studied by analyzing 638 cross-coincidence histograms as functions of stimulus type, stimulus level, and estimated neuron distance. Significance criteria for correlograms were established on the basis of the distribution of extreme values in a large number of correlograms for nonsimultaneously recorded pairs. 3. Simultaneous recordings from three neurons, that all showed significant neural pair correlations were analyzed with the use of the joint occurrence diagram, which displays the joint coincidences for the firings of two units (a and b) with the firings of the trigger unit (c). 4. It was found that 97.5% of the pairs showed a significant stimulus-induced correlation; neighboring neurons exhibited a stronger stimulus correlation (synchrony) than more distant neurons. 5. Positive neural interaction strength (75% to shared excitatory input) was independent of neuron distance (taking into account that the estimated electrode distance in the present investigation was never greater than 300 microns) and occurred in 25% of the pairs investigated. About 25% of the positive neural correlations could be attributed to unidirectional excitation, the majority of which was found for single-electrode pairs. Negative neural correlation occurred in 8% of the pairs and, with one exception, was found only for neurons recorded on the same electrode. 6. Evidence for the presence of feed-forward and/or feedback inhibition was found. 7. There was a strong stimulus-type influence on stimulus correlation and on positive neural correlation, whereas stimulus intensity affected the stimulus correlation but not the neural correlation. 8. From the incidence of triplet correlations, it was concluded that the divergence of afferents onto midbrain neurons was limited; it was unlikely that more than three neurons were contacted by one afferent. In contrast, convergence of afferents on torus semicircularis cells was widespread; 40-50% of the midbrain neurons were bimodally tuned and received input originating from the two auditory papillae. Convergence of fibers from the same papilla was also extensive. 9. Fast modulation of functional neural connectivity through the activity of other neurons was found, although this was probably not the result of actual changes in synaptic strength but of synchronized changes in firing rate.

Acoustic Stimulation↗
PubMed1995

Investigation of the role of an amino acid triplet repeat in differentiating drug-receptor interaction at m1 and m2 muscarinic receptors.

The first putative extracellular domains of both m1 and m2 muscarinic receptors contain a triplet of amino acid residues consisting of leucine (L), tyrosine (Y), and threonine (T). This triplet is repeated as LYTLYT in m2 receptors. However, it is repeated in a transposed fashion (LYTTYL) in the sequence of m1 receptors. In this work we employed site-directed mutagenesis to investigate the possible significance of this unique sequence diversity in determining the distinct differential drug-receptor interaction at the two receptor subtypes. Mutation of the LYTTYL sequence of m1 receptors to the corresponding m2 receptor LYTLYT sequence, however, did not significantly change the binding affinity of the agonist carbachol or the affinity of the majority of a series of receptor antagonists which are able to discriminate between wild-type m1 and m2 receptors. The reverse mutation at the m2 receptor also did not modify agonist affinity, but altered affinity of several receptor subtype-selective antagonists. The magnitude of affinity changes, however, was small, and the direction of these changes was opposite to what would be expected if the m2 receptor LYTLYT seqence were important for determining the binding profile of m2-receptor-selective antagonists. Our data suggest that the LYTTYL-LYTLYT sequence differences between ml and m2 muscarinic receptors are not important for determining receptor pharmacology.

Amino Acid Sequence↗
PubMed2005

Shortest triplet clustering: reconstructing large phylogenies using representative sets.

BACKGROUND: Understanding the evolutionary relationships among species based on their genetic information is one of the primary objectives in phylogenetic analysis. Reconstructing phylogenies for large data sets is still a challenging task in Bioinformatics. RESULTS: We propose a new distance-based clustering method, the shortest triplet clustering algorithm (STC), to reconstruct phylogenies. The main idea is the introduction of a natural definition of so-called k-representative sets. Based on k-representative sets, shortest triplets are reconstructed and serve as building blocks for the STC algorithm to agglomerate sequences for tree reconstruction in O(n2) time for n sequences. Simulations show that STC gives better topological accuracy than other tested methods that also build a first starting tree. STC appears as a very good method to start the tree reconstruction. However, all tested methods give similar results if balanced nearest neighbor interchange (BNNI) is applied as a post-processing step. BNNI leads to an improvement in all instances. The program is available at http://www.bi.uni-duesseldorf.de/software/stc/. CONCLUSION: The results demonstrate that the new approach efficiently reconstructs phylogenies for large data sets. We found that BNNI boosts the topological accuracy of all methods including STC, therefore, one should use BNNI as a post-processing step to get better topological accuracy.

Algorithms↗
PubMed2006

Fast estimation of the difference between two PAM/JTT evolutionary distances in triplets of homologous sequences.

BACKGROUND: The estimation of the difference between two evolutionary distances within a triplet of homologs is a common operation that is used for example to determine which of two sequences is closer to a third one. The most accurate method is currently maximum likelihood over the entire triplet. However, this approach is relatively time consuming. RESULTS: We show that an alternative estimator, based on pairwise estimates and therefore much faster to compute, has almost the same statistical power as the maximum likelihood estimator. We also provide a numerical approximation for its variance, which could otherwise only be estimated through an expensive re-sampling approach such as bootstrapping. An extensive simulation demonstrates that the approximation delivers precise confidence intervals. To illustrate the possible applications of these results, we show how they improve the detection of asymmetric evolution, and the identification of the closest relative to a given sequence in a group of homologs. CONCLUSION: The results presented in this paper constitute a basis for large-scale protein cross-comparisons of pairwise evolutionary distances.

Algorithms↗
PubMed2003

Monochorionic-triamniotic triplet pregnancy after intracytoplasmic sperm injection, assisted hatching, and two-embryo transfer: first reported case following IVF.

BACKGROUND: We present a case of monochorionic-triamniotic pregnancy that developed after embryo transfer following in vitro fertilization (IVF). METHODS: After controlled ovarian hyperstimulation and transvaginal retrieval of 22 metaphase II oocytes, fertilization was accomplished with intracytoplasmic sperm injection (ICSI). Assisted embryo hatching was performed, and two embryos were transferred in utero. One non-transferred blastocyst was cryopreserved. RESULTS: Fourteen days post-transfer, serum hCG level was 423 mIU/ml and subsequent transvaginal ultrasound revealed a single intrauterine gestational sac with three separate amnion compartments. Three distinct foci of cardiac motion were detected and the diagnosis was revised to monochorionic-triamniotic triplet pregnancy. Antenatal management included cerclage placement at 19 weeks gestation and hospital admission at 28 weeks gestation due to mild preeclampsia. Three viable female infants were delivered via cesarean at 30 5/7 weeks gestation. CONCLUSIONS: The incidence of triplet delivery in humans is approximately 1:6400, and such pregnancies are classified as high-risk for reasons described in this report. We also outline an obstetric management strategy designed to optimize outcomes. The roles of IVF, ICSI, assisted embryo hatching and associated laboratory culture conditions on the subsequent development of monozygotic/monochorionic pregnancy remain controversial. As demonstrated here, even when two-embryo transfer is employed after IVF the statistical probability of monozygotic multiple gestation cannot be reduced to zero. We encourage discussion of this possibility during informed consent for the advanced reproductive technologies.

Journal Article↗
PubMed2003

Cisplatin plus gemcitabine versus a cisplatin-based triplet versus nonplatinum sequential doublets in advanced non-small-cell lung cancer: a Spanish Lung Cancer Group phase III randomized trial.

PURPOSE: To compare the survival benefit obtained with cisplatin plus gemcitabine, a cisplatin-based triplet, and nonplatinum sequential doublets in advanced non-small-cell lung cancer (NSCLC). PATIENTS AND METHODS: Stage IIIB to IV NSCLC patients were randomly assigned to receive cisplatin 100 mg/m2 day 1 plus gemcitabine 1,250 mg/m2 days 1 and 8, every 3 weeks for six cycles (CG); cisplatin 100 mg/m2 day 1 plus gemcitabine 1,000 mg/m2 and vinorelbine 25 mg/m2 days 1 and 8, every 3 weeks for six cycles (CGV); or gemcitabine 1,000 mg/m2 plus vinorelbine 30 mg/m2 days 1 and 8, every 3 weeks for three cycles, followed by vinorelbine 30 mg/m2 days 1 and 8 plus ifosfamide 3 g/m2 day 1, every 3 weeks for three cycles (GV-VI). RESULTS: Five hundred fifty-seven patients were assigned to treatment (182 CG, 188 CGV, 187 GV-VI). Response rates were significantly inferior for the nonplatinum sequential doublet (CG, 42%; CGV, 41%; GV-VI, 27%; CG v GV-VI, P =.003). No differences in median survival or time to progression were observed. Toxicity was higher for the triplet: grade 3 to 4 neutropenia (GC, 32%; CGV, 57%; GV-VI, 27%; P <.05); neutropenic fever (CG, 4%; CGV, 19%; GV-VI, 5%; P <.0001); grade 3 to 4 thrombocytopenia (CG, 19%; CGV, 23%; GV-VI, 3%; P =.0001); and grade 3 to 4 emesis (GC, 22%; GCV, 32%; GV-VI, 6%; P <.0001). CONCLUSION: On the basis of these results, CG remains a standard regimen for first-line treatment of advanced NSCLC.

Adult↗
PubMed1998

Roles of head and tail domains in alpha-internexin's self-assembly and coassembly with the neurofilament triplet proteins.

The roles of the head and tail domains of alpha-internexin, a type IV neuronal intermediate filament protein, in its self-assembly and coassemblies with neurofilament triplet proteins, were examined by transient transfections with deletion mutants in a non-neuronal cell line lacking an endogenous cytoplasmic intermediate filament network. The results from the self-assembly studies showed that the head domain was essential for alpha-internexin's ability to self-assemble into a filament network and the tail domain was important for establishing a proper filament network. The data from the coassembly studies demonstrated that alpha-internexin interacted differentially with the neurofilament triplet protein subunits. Wild-type NF-L or NF-M, but not NF-H, was able to complement and form a normal filament network with the tailless alpha-internexin mutant, the alpha-internexin head-deletion mutant, or the alpha-internexin mutant missing the entire tail and some amino-terminal portion of the head domain. In contrast, neither the tailless NF-L mutant nor the NF-L head-deletion mutant was able to form a normal filament network with any of these alpha-internexin deletion mutants. However, coassembly of the tailless NF-M mutant with the alpha-internexin head-deletion mutant and coassembly of the NF-M head-deletion mutant with the tailless alpha-internexin mutant resulted in the formation of a normal filament network. Thus, the coassembly between alpha-internexin and NF-M exhibits some unique characteristics previously not observed with other intermediate filament proteins: only one intact tail and one intact head are required for the formation of a normal filament network, and they can be present within the same partner or separately in two partners.

Actin Cytoskeleton↗
PubMed2004

Caenorhabditis elegans as a model system for triplet repeat diseases.

Common features underlie the generation and function of neurons in multicellular animals. It is likely that conserved pathways and genes also are involved in neuronal degeneration and malfunction. To address the molecular mechanisms of complex human neurological disorders, many investigators are choosing to study these diseases in simpler organisms. The nematode Caenorhabditis elegans provides an excellent model system to address genetically the mechanisms of triplet repeat diseases. Advantages of using C. elegans as a model system include the ease of genetic manipulation, the sequenced genome, and a short life cycle. Furthermore, researchers can precisely identify specific neurons and follow their development or survival throughout the animal's lifetime. This chapter describes the tools and approaches for modeling triplet repeat diseases in C. elegans with a specific emphasis on polyglutamine (polyQ) diseases. Although the bulk of the chapter is devoted to generating a polyQ disease model in C. elegans, it also addresses potential avenues for assessing the impact of specific candidate genes/pathways on the disease process, including cell death and aging.

Animals↗
PubMed1997

Conjoined twins in a triplet pregnancy.

Conjoined twins in a triplet pregnancy is an extremely rare occurrence. We present here, a 27-year-old multigravida with gestational diabetes and a conjoined twins in a triplet pregnancy.

Adult↗
PubMed2000

[Ca II triplet equivalent widths of spiral galaxy M31 and elliptical galaxy M32].

The Calcium II triplet (Ca II T) lines in the near infrared spectral region is very important feature for late type stars, which serves as an important metallicity indicator for such stars. This is also true for stellar systems composed mainly of late type stars, such as old stellar clusters and galaxies. In this work, we made observations of the very famous spiral galaxy M31 and its dwarf elliptical companion M32, using the OMR spectrograph attached to the 2.16-meter telescope in Beijing Astronomical Observatory. Near-infrared spectra of the nuclear and disk regions on M31, as well as two slices along the major and the minor axis of M32, are derived. Equivalent widths of the Ca II triplet lines are measured using normal astrophysical spectrum analyzing techniques. The results are fundamental data for these two galaxies, which can be applied to researches for stellar population analysis of these galaxies.

English Abstract↗