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Results for “Condensates”

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At least 289 records · Page 16Linked to original sources

PubMed1999

DNA toroids: stages in condensation.

The effects of polylysine (PLL) and PLL-asialoorosomucoid (AsOR) on DNA condensation have been analyzed by AFM. Different types of condensed DNA structures were observed, which show a sequence of conformational changes as circular plasmid DNA molecules condense progressively. The structures range from circular molecules with the length of the plasmid DNA to small toroids and short rods with approximately 1/6 to 1/8 the contour length of the uncondensed circular DNA. Single plasmid molecules of 6800 base pairs (bp) condense into single toroids of approximately 110 nm diameter, measured center-to-center. The results are consistent with a model for DNA condensation in which circular DNA molecules fold several times into progressively shorter rods. Structures intermediate between toroids and rods suggest that at least some toroids may form by the opening up of rods as proposed by Dunlap et al. [(1997) Nucleic Acids Res. 25, 3095]. Toroids and rods formed at lysine:nucleotide ratios of 5:1 and 6:1. This high lysine:nucleotide ratio is discussed in relation to entropic considerations and the overcharging of macroions. PLL-AsOR is much more effective than PLL alone for condensing DNA, because several PLL molecules are attached to a single AsOR molecule, resulting in an increased cation density.

Asialoglycoproteins↗

PubMed2006

Electrostatic, steric, and hydration interactions favor Na(+) condensation around DNA compared with K(+).

Condensation of monovalent counterions around DNA influences polymer properties of the DNA chain. For example, the Na(+) ions show markedly stronger propensity to induce multiple DNA chains to assemble into compact structures compared with the K(+) ions. To investigate the similarities and differences in the sodium and potassium ion condensation around DNA, we carried out a number of extensive all-atom molecular dynamics simulations of a DNA oligomer consisting of 16 base pairs, [d(CGAGGTTTAAACCTCG)](2), in explicit water. We found that the Na(+) ions penetrate the DNA interior and condense around the DNA exterior to a significantly larger degree compared with the K(+) ions. We have provided a microscopic explanation for the larger Na(+) affinity toward DNA that is based on a combination of steric, electrostatic, and hydration effects. Unexpectedly, we found that the Cl(-) co-ions provide more efficient electrostatic screening for the K(+) ions than for the Na(+) ions, contributing to the larger Na(+) condensation around DNA. To examine the importance of the discrete nature of water and ions, we also computed the counterion distributions from the mean-field electrostatic theory, demonstrating significant disagreements with the all-atom simulations. Prior experimental results on the relative extent of the Na(+) and K(+) condensation around DNA were somewhat contradictory. Recent DNA compaction experiments may be interpreted to suggest stronger Na(+) condensation around DNA compared to K(+), which is consistent with our simulations. We also provide a simple interpretation for the experimentally observed increase in DNA electrophoretic mobility in the alkali metal series, Li(+) < Na(+) < K(+) < Rb(+). We compare the DNA segment conformational preferences in various buffers with the proposed NMR models.

DNA↗

PubMed2005

DNA psi-condensation and reentrant decondensation: effect of the PEG degree of polymerization.

Psi-condensation of DNA fragments of about 4 kbp was induced by poly(ethylene glycol) (PEG), with degrees of polymerization ranging from 45 to 182, and univalent salt (NaCl). Using circular dichroism spectroscopy, we were able to accurately determine the critical amount of PEG needed to induce condensation, as a function of the NaCl concentration. A significant dependence on the PEG degree of polymerization was found. Phase boundaries determined for the multimolecular condensation were very similar to those observed previously for the monomolecular collapse, with two asymptotic regimes at low and high salt concentrations. We analyze our data using a theoretical model that properly takes into account both the polyelectrolyte nature of the DNA and the liquid crystallinity of the condensed phase. The model assumes that all PEG is excluded from the condensates and shows reentrant decondensation only at low salt. We also systematically study reentrant decondensation and find a very strong dependence on PEG molecular weight. At low PEG molecular weight, decondensation occurs at relatively low concentrations of PEG, and over a wide range of salt concentrations. This suggests that in the reentrant decondensation the flexible polymers used are not completely excluded from the condensed phase.

Chemical Phenomena↗

PubMed2006

A gas- and condensed-phase density functional study of donor-acceptor complexes of sulfur trioxide.

A series of donor-acceptor complexes containing sulfur trioxide have been studied in the gas and condensed phases using density functional theory. The condensed phase is represented using the polarizable continuum model. The systems investigated include complexes of nitrogen-containing donor molecules, (CH(3))(n)H(3-n)N (n = 0-3), with SO(3) and complexes of oxygen-containing donor molecules, (CH(3))(m)H(2-m)O (m = 0-2), with SO(3). Significant differences are observed between the gas- and condensed-phase properties of the complexes as a result of the ability of the condensed-phase medium to support higher charge separation between the donor and acceptor. The gas/condensed-phase behavior of two nitrogen-containing complexes, (CH(3))H(2)N-SO(3) and (CH(3))(2)HN-SO(3), has been investigated for the first time. These complexes exhibit properties intermediate to the previously observed H(3)N-SO(3) and (CH(3))(3)N-SO(3) complexes. Systematic trends in the gas- and condensed-phase structure and properties have been observed as methyl groups are added to the donor molecule. In addition, two oxygen-containing complexes, CH(3)OH-SO(3) and (CH(3))(2)O-SO(3), have been characterized for the first time. The differences between the gas- and condensed-phase properties of the oxygen-containing complexes are, in many cases, larger than those of the nitrogen-containing complexes, and therefore they represent an intriguing new class of complexes for potential experimental observation. Finally, a strong correlation between the charge transfer and binding energy has been obtained for both the nitrogen- and oxygen-containing complexes of sulfur trioxide.

Journal Article↗

PubMed1998

Stability of peptide-condensed plasmid DNA formulations.

Low molecular weight homogeneous peptides were used to form peptide/DNA condensates. A peptide possessing 18 lysines was found to protect plasmid DNA from serum endonuclease and sonicative-induced degradation whereas a shorter peptide possessing 8 lysines dissociated in 0.1 M sodium chloride and failed to protect DNA from enzymatic degradation. Peptide-condensed DNA showed no change in the ratio of supercoiled to circular DNA following 100 W sonication for up to 60 s and was able to transfect HepG2 cells with equivalent efficiency as untreated condensed plasmid DNA. Alternatively, uncondensed plasmid DNA was rapidly fragmented by sonication and serum endonucleases and resulted in negligible gene expression following condensation with peptide. Cationic lipid/DNA complexes were only partially effective at stabilizing DNA in serum compared to the complete stabilization afforded by peptide/DNA condensation. These results indicate that the stabilization afforded by condensation with a peptide protects DNA during formulation and preserves its structure in serum. These functions are important to achieve optimal gene expression from a nonviral gene delivery system.

Animals↗

PubMed2007

Condensing effect of palmitic acid on DPPC in mixed Langmuir monolayers.

The interaction between deuterated dipalmitoylphosphatidylcholine (DPPC-d62) and palmitic acid (PA) in mixed Langmuir monolayers is studied using vibrational sum frequency generation (VSFG) spectroscopy. Palmitic acid is an additive in exogenous lung surfactant preparations such as Survanta and Surfaxin. The effect of PA on the chain conformation and orientation of DPPC in the liquid-expanded and condensed phases is explored. A condensing effect of PA on DPPC is observed with VSFG. At 12 mN/m, DPPC-d62 alone is in the liquid-expanded phase. Adding PA increases the conformational ordering of DPPC chains and causes DPPC to transition from the expanded phase into the condensed phase. At 42 mN/m, DPPC-d62 and PA form a mixed structure in the condensed phase. The presence of PA decreases the chain tilt angle of DPPC, increasing the orientational ordering of DPPC chains. At 42 mN/m, there is also evidence from the frequency red shift of the PO2- symmetric stretch that the carboxyl group of PA forms a hydrogen bond with the phosphate group of DPPC in the condensed phase. From this work the effect of PA on DPPC is 2-fold: (1) PA increases the chain ordering of DPPC and promotes the LE and TC phase separation and (2) due to the miscibility between DPPC and PA in the condensed phase, PA decreases the collapse pressure.

Journal Article↗

PubMed1998

Meiotin-1, a meiosis-enriched protein present in normal leptotene chromosomes and lacking in precociously condensed leptotene chromosomes.

During mitotic prophase, chromosomes progressively compact to their metaphase length. In contrast, meiotic chromosomes condense moderately until late in prophase I, then they condense more dramatically (coil) to their fully condensed state. Meiotin-1 is a meiosis-enriched, chromosomal protein. We propose that it delays coiling until after reciprocal genetic exchange. We have used immunoblotting and immunocytochemistry with normal lily cells undergoing meiosis to demonstrate that meiotin-1 is present during the early portions of prophase I, but diminishes at the time when meiotic chromosomes begin to coil. Additionally, we have examined lily meiotic nuclei undergoing the reversible phenomenon of precocious leptotene chromosome condensation (precocious coiling). The leptotene chromosomes that are precociously condensed lack meiotin-1 immunostaining. Furthermore nuclei returning to the normal state of moderate prophase I condensation acquire meiotin-1.

Antibodies, Monoclonal↗

PubMed1989

Focal points for chromosome condensation and decondensation revealed by three-dimensional in vivo time-lapse microscopy.

Although the dynamic behaviour of chromosomes has been extensively studied in their condensed state during mitosis, chromosome behaviour during the transition to and from interphase has not been well documented. Previous electron microscopic studies suggest that chromosomes condense in a non-uniform fashion at the nuclear periphery. But chromosome condensation is a complicated and dynamic process and requires continuous observation in living tissues to be fully understood. Using a recently developed three-dimensional time-lapse fluorescence microscopy technique, we have observed chromosomes as they relax from telophase, through interphase, until their condensation at the next prophase. This technique has been improved to produce higher-resolution images by implementing new stereographic projection and computational processing protocols. These studies have revealed that chromosomal regions on the nuclear envelope, distinct from the centromeres and telomeres, serve as foci for the decondensation and condensation of diploid chromosomes. The relative positions of the late decondensation sites at the beginning of interphase appear to correspond to the early condensation sites at the subsequent prophase.

Animals↗

PubMed2000

The Grapes checkpoint coordinates nuclear envelope breakdown and chromosome condensation.

Mutations in the embryonic Drosophila Grapes/Chk1 checkpoint result in an abbreviated interphase, chromosome condensation defects and metaphase delays. To clarify the relationship between these phenotypes, we simultaneously timed multiple nuclear and cytoplasmic events in mutant grp-derived embryos. These studies support a model in which grp disrupts an S-phase checkpoint, which results in progression into metaphase with incompletely replicated chromosomes. We also show that chromosome condensation is independent of the state of DNA replication in the early embryo. Therefore, grp condensation defects are not a direct consequence of entering metaphase with incompletely replicated chromosomes. Rather, initiation of chromosome condensation (ICC) occurs at the normal time in grp-derived embryos, but the shortened interval between ICC and metaphase does not provide sufficient time to complete condensation. Our results suggest that these condensation defects, rather than incomplete DNA replication, are responsible for the extensive metaphase delays observed in grp-derived embryos. This analysis provides an example of how the loss of a checkpoint can disrupt the timing of multiple events not directly monitored by that checkpoint. These results are likely to apply to vertebrate cells and suggest new strategies for destroying checkpoint-compromised cancer cells.

Animals↗

PubMed2000

Direct observation of growth and collapse of a Bose-Einstein condensate with attractive interactions.

Quantum theory predicts that Bose-Einstein condensation of a spatially homogeneous gas with attractive interactions is precluded by a conventional phase transition into either a liquid or solid. When confined to a trap, however, such a condensate can form, provided that its occupation number does not exceed a limiting value. The stability limit is determined by a balance between the self-attractive forces and a repulsion that arises from position-momentum uncertainty under conditions of spatial confinement. Near the stability limit, self-attraction can overwhelm the repulsion, causing the condensate to collapse. Growth of the condensate is therefore punctuated by intermittent collapses that are triggered by either macroscopic quantum tunnelling or thermal fluctuation. Previous observations of growth and collapse dynamics have been hampered by the stochastic nature of these mechanisms. Here we report direct observations of the growth and subsequent collapse of a 7Li condensate with attractive interactions, using phase-contrast imaging. The success of the measurement lies in our ability to reduce the stochasticity in the dynamics by controlling the initial number of condensate atoms using a two-photon transition to a diatomic molecular state.

Journal Article↗

PubMed2001

Bose-Einstein condensation on a microelectronic chip.

Although Bose-Einstein condensates of ultracold atoms have been experimentally realizable for several years, their formation and manipulation still impose considerable technical challenges. An all-optical technique that enables faster production of Bose-Einstein condensates was recently reported. Here we demonstrate that the formation of a condensate can be greatly simplified using a microscopic magnetic trap on a chip. We achieve Bose-Einstein condensation inside the single vapour cell of a magneto-optical trap in as little as 700 ms-more than a factor of ten faster than typical experiments, and a factor of three faster than the all-optical technique. A coherent matter wave is emitted normal to the chip surface when the trapped atoms are released into free fall; alternatively, we couple the condensate into an 'atomic conveyor belt', which is used to transport the condensed cloud non-destructively over a macroscopic distance parallel to the chip surface. The possibility of manipulating laser-like coherent matter waves with such an integrated atom-optical system holds promise for applications in interferometry, holography, microscopy, atom lithography and quantum information processing.

Journal Article↗

PubMed1999

Acinus is a caspase-3-activated protein required for apoptotic chromatin condensation.

Apoptosis is defined by several unique morphological nuclear changes, such as chromatin condensation and nuclear fragmentation. These changes are triggered by the activation of a family of cysteine proteases called caspases, and caspase-activated DNase (CAD/DFF40) and lamin protease (caspase-6) have been implicated in some of these changes. CAD/DFF40 induces chromatin condensation in purified nuclei, but distinct caspase-activated factor(s) may be responsible for chromatin condensation. Here we use an in vitro system to identify a new nuclear factor, designated Acinus, which induces apoptotic chromatin condensation after cleavage by caspase-3 without inducing DNA fragmentation. Immunodepletion experiments showed that Acinus is essential for apoptotic chromatin condensation in vitro, and an antisense study revealed that Acinus is also important in the induction of apoptotic chromatin condensation in cells.

Amino Acid Sequence↗

PubMed1977

Studies on the local and systemic carcinogenicity of topically applied smoke condensate from a substitute smoking material.

The topical carcinogenicity to mouse skin of smoke condensates obtained from a tobacco substitute (NSM), alone or in combination with tobacco, has been compared with condensate from tobacco and with acetone, the solvent used. Sixteen different types of cigarette were used to make the condensates, and the age-standardized results have been analysed according to the Weibull distribution model. The results show that NSM condensate has less than 25% of the potency of tobacco condensate (37% at 95% upper confidence limit), and that condensates from blends of NSM and tobacco are similarly reduced in activity. General pathology analysis failed to reveal abnormalities due to NSM.

Animals↗

PubMed2026

NAP1 switches from an activator to a limiter of interferon induction by trapping TBK1 in condensates.

TBK1 kinase is a central regulator of type I IFN production. Upon activation of the IFN-β induction pathway, TBK1-adaptor proteins (NAP1, SINTBAD, TANK) form liquid condensates. We show that NAP1 condensates concentrate TBK1. Using NAP1KO cell lines, we demonstrate that NAP1 exerts a dual effect on TBK1 activity. Initially, NAP1 binds TBK1 and increases its activity, promoting IFN pathway activation. Subsequently, TBK1-mediated phosphorylation of NAP1 induces the formation of condensates. These NAP1 condensates concentrate both TBK1 and the phosphatase PP2A, which dephosphorylates and consequently deactivates TBK1, thus limiting IFN induction. Additionally, in patients with lupus or interferonopathies, we identify NAP1 variants unable to form condensates upon danger signal exposure, which sustain TBK1 activation without limiting its activity. This study reveals a mode of regulating a signaling pathway through condensate formation and provides a potential molecular explanation for immune dysregulation associated with NAP1 variants in certain patients with interferonopathies.

Protein Serine-Threonine Kinases↗

PubMed2005

Akt phosphorylates acinus and inhibits its proteolytic cleavage, preventing chromatin condensation.

Akt promotes cell survival by phosphorylating and inhibiting components of the intrinsic cell death machinery. Akt translocates into the nucleus upon exposure of cells to survival factors, but little is known about its functions in the nucleus. Here, we show that acinus, a nuclear factor required for apoptotic chromatin condensation, is a direct target of Akt. We demonstrate that Akt phosphorylation of acinus on serine 422 and 573 results in its resistance to caspase cleavage in the nucleus and the inhibition of acinus-dependent chromatin condensation. Abolishing acinus phosphorylation by Akt through mutagenesis accelerates its proteolytic degradation and chromatin condensation. Acinus S422, 573D, a mutant mimicking phosphorylation, resists against apoptotic cleavage and prevents chromatin condensation. Knocking down of acinus substantially decreases chromatin condensation, and depletion of Akt provokes the apoptotic cleavage of acinus. Thus, Akt inhibits chromatin condensation during apoptosis by phosphorylating acinus in the nucleus, revealing a specific mechanism by which nuclear Akt promotes cell survival.

Animals↗

PubMed2000

Comparison of cold lateral condensation and a warm multiphase gutta-percha technique for obturating curved root canals.

AIM: The aim of this project was to evaluate and compare the radiographic quality and sealability of root fillings in extracted human teeth using lateral condensation of gutta-percha or multiphase gutta-percha obturation (Alphaseal). METHODOLOGY: A total of 108 freshly extracted human, mature single-rooted teeth were divided into two identical groups of 54 teeth on the basis of root canal shape. The canals were prepared to a minimum 0.055 taper and enlarged to size 35 at the apex. All root canals were flushed with 17% EDTA solution and 2.5% NaOCl to remove the dentinal smear layer. The canals of one group were obturated using cold lateral condensation of gutta-percha and the canals of the other group were filled using a warm multiphase gutta-percha obturation technique. The extrusion of sealer and/or gutta-percha through the apex of the teeth was recorded using a simple yes/no scheme. The sealability of each technique was assessed by a dye penetration method. The radiographic quality of obturation was determined for each canal using a four-point scale. RESULTS: Root canals filled by multiphase obturation had significantly more extrusion of sealer (P < 0.001) and gutta-percha (P < 0.001) than canals filled by lateral condensation. Canals filled by multiphase gutta-percha obturation had significantly less apical dye leakage than those obturated by lateral condensation (P < 0.05). Lateral condensation achieved significantly better scores for radiographic quality than multiphase obturation from the bucco-lingual view (P < 0.01). CONCLUSIONS: Under laboratory conditions multiphase gutta-percha had better sealability but poorer radiographic quality than lateral condensation.

Composite Resins↗

PubMed2001

Novel evidence for apoptotic cell response and differential signals in chromatin condensation and DNA cleavage in victorin-treated oats.

Histological and cytological evidence of where and when apoptotic cells occur in Pc-2/Vb oat cells treated with victorin was obtained by observing DNA strand breaks at both light (LM) and electron microscope (EM) levels using TUNEL techniques. DNA from leaf segments that had been floated on victorin solution with the abaxial epidermis removed showed typical ladders on agarose gels. Nuclear chromatin condensation, followed by cell collapse, started in the mesophyll cells closest to the victorin solution. LM-TUNEL was positive in the non-collapsed cells but not in the collapsed cells in the treated leaves. However, the EM-TUNEL assay was positive in the nuclei of the non-collapsed as well as the collapsed cells where nuclear fragments dispersed into the cytoplasm, and the immunogold density was much higher than that in the cells killed by a high concentration of H2O2, suggesting that the victorin-treated collapsed cells are in the last stage of apoptotic cell death. The immunogold labelling in the victorin-treated non-collapsed cells was restricted to condensed heterochromatin, indicating that chromatin condensation is associated with DNA cleavage. Pharmacological studies indicated that proteases and nucleases may play a role in the apoptotic response. However, the EM-TUNEL assay indicated that EGTA co-incubated with victorin blocked DNA cleavage, but failed to prevent chromatin condensation. Moreover, protein kinases were involved in chromatin condensation, but did not affect DNA digestion, suggesting that chromatin condensation and DNA cleavage are differentially regulated in the death process in oats.

Apoptosis↗

PubMed2001

Comparison of lateral condensation and thermomechanically compacted warm alpha-phase gutta-percha with a single cone for obturating curved root canals.

OBJECTIVE: To evaluate and compare the sealability and radiographic quality of root fillings in extracted teeth by using lateral condensation of gutta-percha or alpha-phase gutta-percha in conjunction with a single gutta-percha cone. STUDY DESIGN: A total of 108 single-rooted teeth were divided into 2 groups of 54 teeth based on canal shape. Canals were prepared to a minimum 0.055 taper and enlarged to a size 35 at the working distance. Irrigation was done with 17% EDTA and 2.5% sodium hypochlorite (NaOCl) to remove smear layer. One group was obturated by using cold lateral condensation of gutta-percha; the other group was obturated with thermomechanically compacted alpha-phase gutta-percha and a single cone of gutta-percha. Apical extrusion of sealer or gutta-percha was recorded. Sealability of each technique was assessed by dye penetration. The radiographic quality of obturation was also determined. RESULTS: Root canals filled with alpha-phase gutta-percha and a single cone had significantly more extrusion of sealer than canals filled by lateral condensation. Lateral condensation achieved significantly better scores for radiographic quality. There was no significant difference between the 2 filling techniques in terms of apical or coronal leakage. CONCLUSIONS: Thermomechanically condensed alpha-phase gutta-percha used in conjunction with a single gutta-percha cone had poorer radiographic quality than laterally condensed gutta-percha.

Dental Leakage↗