DNA KNOT FORMATION IN AQUEOUS SOLUTIONS

1994 ◽  
Vol 03 (03) ◽  
pp. 287-298 ◽  
Author(s):  
STANLEY Y. SHAW ◽  
JAMES C. WANG
Keyword(s):  
Aqueous Solutions ◽  
Experimental Test ◽  
Attractive Potential ◽  
Sodium Ions ◽  
Magnesium Ions ◽  
Close Apposition ◽  
Closed Chain ◽  
Solvent Properties

The knotting probability of a closed chain has been calculated as a function of chain dimensions and solvent properties in a number of studies. We have measured the probability of DNA knot formation upon random cyclization of linear DNA in vitro to provide an experimental test of the various theoretical treatments of the problem; parameters of these models, such as the effective chain diameter of DNA, were calculated in different concentrations of counterions. Our results in the presence of sodium ions agree well with theoretical treatments of DNA as a polyelectrolyte; knotting data in the presence of divalent magnesium ions indicate that moderate concentrations of magnesium ions can induce an attractive potential between DNA segments, resulting in negative values of the calculated effective DNA helix diameter. We discuss structures in which the divalent magnesium counterion facilitates the close apposition of two DNA segments, and review the effect of chemical- and protein-mediated crosslinks between DNA segments on DNA knot formation. Finally, we consider DNA knot formation in vivo.

scholarly journals Absorption of lactulose from mammalian gastrointestinal tract

1979 ◽  
Vol 41 (1) ◽  
pp. 47-51 ◽  
Author(s):  
D. F. Evered ◽  
F. Sadoogh-Abasian
Keyword(s):  
Small Intestine ◽  
Calcium Ions ◽  
Clinical Evidence ◽  
Buccal Cavity ◽  
Rat Small Intestine ◽  
Sodium Ions ◽  
Mode Of Transport ◽  
Poor Absorption

1. The disaccharide lactulose (galactosyl-β-1,4-fructose) was poorly absorbed from rat small intestine in vitro and human mouth in vivo.2. These results confirm indirect clinical evidence of poor absorption from the intestine.3. The presence of calcium ions, or absence of sodium ions, had no effect on lactulose absorption from the buccal cavity.4. The presence of ouabain, or absence of Na+, did not decrease the absorption of lactulose from small intestine.5. It is thought that the mode of transport, in both instances, is by passive diffusion with the concentration gradient.

scholarly journals Experimental Test of the Importance of Preen Oil in Rock Doves (Columba Livia)

The Auk ◽  
2003 ◽  
Vol 120 (2) ◽  
pp. 490-496 ◽  
Author(s):  
BrettR. Moyer ◽  
Alex N. Rock ◽  
Dale H. Clayton
Keyword(s):  
Experimental Test ◽  
Columba Livia ◽  
Uropygial Gland ◽  
Preen Gland ◽  
In Vivo Experiments ◽  
Preen Oil ◽  
Bacteria And Fungi

Abstract Most species of birds have a uropygial gland, also known as a preen gland, which produces oil that birds spread through their plumage when preening. The plumage of waterfowl deprived of uropygial oil becomes brittle and is subject to breakage. For other groups of birds, however, the importance of preen oil remains unclear. Previous workers have argued that preen oil may serve little or no function in Columbiforms (pigeons and doves). We tested that assertion by removing uropygial glands from Rock Doves (Columba livia) and assessing their plumage condition after several months. The results of that experiment showed significant degradation of plumage in the absence of oil. Our results are the first rigorous demonstration that preen oil is important for plumage condition in nonwaterfowl. We tested one possible function of preen oil—that it has insecticidal properties and that reduction in plumage condition on birds without glands is due to an increase in ectoparasites. We tested that hypothesis for feather-feeding lice (Phthiraptera:Ischnocera) using both in vitro and in vivo experiments. Lice raised in an incubator died more rapidly on feathers with preen oil than on feathers without oil, which suggests that preen oil may help combat lice. However, removal of the preen gland from captive birds had no significant effect on louse loads over the course of a four-month experiment. Although the results of our in vivo experiments suggest that preen oil may not be an important defense against lice, further experiments are needed. We also consider the possibility that preen oil may protect birds against other plumage-degrading organisms, such as bacteria and fungi.

scholarly journals Hematin-derived anticoagulant. Generation in vitro and in vivo.

1986 ◽  
Vol 163 (3) ◽  
pp. 724-739 ◽  
Author(s):  
R L Jones
Keyword(s):  
Aqueous Solutions ◽  
Anticoagulant Activity ◽  
Parent Compound ◽  
Iron Chelator ◽  
Ferric Citrate ◽  
Anticoagulant Effect ◽  
Single Peak

Prolongation of clotting times produced by hematin was investigated both in vitro and in vivo. Hematin-derived anticoagulant (HDA) was found to be due to a degradative product or derivative of hematin, and was generated in vitro in standing (aging) aqueous solutions of the parent compound. Generation of HDA in vitro was inhibited by antioxidants. The anticoagulant effect of HDA was inhibited by freshly prepared hematin, fresh Sn-protoporphyrin, imidazole, or the iron chelator desferrioxamine. Ferrioxamine did not inhibit HDA, and inhibition by imidazole was reversed with ferric citrate, suggesting a role for iron in the mechanism of HDA activity. HDA activity was dissociated from hematin in plasma by clotting with thrombin. HDA segregated into the clot fraction, whereas hematin remained largely in the serum fraction, suggesting that HDA may preferentially bind to fibrinogen. TLC and HPLC showed a single peak of HDA activity that was not associated with the parent compound. Evidence for HDA generation in vivo was found when rats were injected with fresh (no HDA) hematin. Prolongation of clotting times appeared after hematin appeared in the plasma, and anticoagulant activity persisted after a fall in plasma hematin concentration. Thus, there was a temporal dissociation between hematin and HDA, suggesting that a modification of hematin must occur in vivo before an anticoagulant effect is produced. Generation of HDA in vitro has implications for hematin preparation and administration. Generation of HDA in vivo suggests that similar modifications of endogenous heme or other porphyrins may occur to produce HDA under physiologic or pathophysiologic conditions.

High Resolution NMR Spectroscopy on Whole-Body Imagers:Optimized Single-and Multi-Pulse Experiments in Vitro

1995 ◽  
Vol 50 (10) ◽  
pp. 942-948
Author(s):  
Fritz Schick
Keyword(s):  
Aqueous Solutions ◽  
Spin Echo ◽  
Single Pulse ◽  
Spin Systems ◽  
The Body ◽  
Coupling Constants ◽  
Whole Body ◽  
Receiver Coil

Abstract From 100 ml spherical glass bottles filled with aqueous solutions and suspended in a homogeneous magnetic field, NMR spectra with linewidths of about 0.7 Hz were achieved in single-pulse and multi-pulse spectra. A relatively wide receiver coil as the body coil or the standard head coil of the manufacturer were employed to acquire spectra after different non-localized pulse sequences. Examples of single-pulse spectra and double spin-echo spectra of aqueous solutions with lactate, citrate, or glucose are demonstrated and discussed. The fact that all experiments can be performed using well-defined pulse angles acting on the entire sample at the field strenght of the whole-body unit allows to determine the characteristics (e.g. chemical shift differences, coupling constants) of spin systems of biologically important molecules precisely, without need for additional spectrometers. Constant flip angles are advantageous for adequate theoretical analysis of spectra from coupled spin systems. The effects of a defined "misadjustment" of the transmitter on the spectra can be measured directly, whereas localized methods always yield a superposition of signals due to the distribution of flip angles inside the selected volume. In some cases, optimized sequence parameters for localized examinations in vivo can be derived numerically from the analyzed coupling data.

scholarly journals Adenine nucleotides and magnesium ions in relation to control of mammalian cerebral-cortex hexokinase

1969 ◽  
Vol 112 (5) ◽  
pp. 579-586 ◽  
Author(s):  
H S Bachelard ◽  
P. S. G. Goldfarb
Keyword(s):  
Mixed Type ◽  
Competitive Inhibition ◽  
Adenine Nucleotides ◽  
Effective Control ◽  
Magnesium Ions ◽  
Soluble Enzyme ◽  
Kinetics Of ◽  
Kinetics Of Inhibition

1. The kinetics of inhibition of brain soluble cytoplasmic hexokinase by ADP were examined in relation to variations in the concentrations of Mg2+ and ATP. The type of inhibition observed was dependent on the Mg2+/ATP ratio. 2. ADP at Mg2+/ATP ratios 2:1 exhibited inhibition of the ‘mixed’ type; at Mg2+/ATP ratios 1:1 the inhibition appeared to be competitive with regard to ATP. 3. Inhibition by free ATP was observed when the Mg2+/ATP ratio was less than 1:1. The inhibition was also of the ‘mixed’ type with respect to MgATP2−. 4. The inhibitions due to ADP and to free ATP were not additive. The results suggested that there may be up to four sites in the soluble enzyme: for glucose, glucose 6-phosphate, ADP and MgATP2−. 5. The ‘free’ non-particulate intracellular Mg2+ concentration was measured and concluded to be about 1·5mm. 6. The concentrations in vivo of Mg2+ and ATP likely to be accessible to a cytoplasmic enzyme are suggested to be below those that yield maximum hexokinase rates in vitro. The enzymic rates were measured at relevant suboptimum concentrations of Mg2+ and ATP in the presence of ADP. Calculations that included non-competitive inhibition due to glucose 6-phosphate (56–65% at 0·25mm) resulted in net rates very similar to the measured rates for overall glycolysis. This system may therefore provide a basis for effective control of cerebral hexokinase.

In vitro activation of murine DRG neurons by CGRP-mediated mucosal mast cell degranulation

2004 ◽  
Vol 287 (1) ◽  
pp. G178-G191 ◽  
Author(s):  
F. De Jonge ◽  
A. De Laet ◽  
L. Van Nassauw ◽  
J. K. Brown ◽  
H. R. P. Miller ◽  
...  
Keyword(s):  
Mast Cell ◽  
Nerve Fibers ◽  
Mast Cell Degranulation ◽  
Mucosal Mast Cell ◽  
Close Apposition ◽  
Drg Neurons ◽  
Nodose Ganglia ◽  
Mouse Mast Cell

Upregulation of CGRP-immunoreactive (IR) primary afferent nerve fibers accompanied by mastocytosis is characteristic for the Schistosoma mansoni-infected murine ileum. These mucosal mast cells (MMC) and CGRP-IR fibers, which originate from dorsal root (DRG) and nodose ganglia, are found in close apposition. We examined interactions between primary cultured MMC and CGRP-IR DRG neurons in vitro by confocal recording of intracellular Ca2+concentration ([Ca2+]i). The degranulatory EC50for the mast cell secretagogue compound 48/80 (C48/80; 10 μg/ml) and the neuropeptides CGRP (2.10−8M) and substance P (SP; 3.10−8M) were determined by measurement of extracellular release of the granule chymase, mouse mast cell protease-1. Application of C48/80 (10 μg/ml) and CGRP and SP (both 10−7M) to Fluo-4-loaded MMC induced a transient rise in [Ca2+]iafter a lag time, indicative of mast cell degranulation and/or secretion. The CGRP response could be completely blocked by pertussis toxin (2 μg/ml), indicating involvement of Giproteins. Application of MMC juice, obtained by C48/80 degranulation of MMC, to Fluo-4-loaded DRG neurons induced in all neurons a rise in [Ca2+]i, indicative of activation. Degranulation of MMC by C48/80 in culture dishes containing Fluo-4-loaded DRG neurons also caused activation of the DRG neurons. In conclusion, these results demonstrate a bidirectional cross-talk between cultured MMC and CGRP-IR DRG neurons in vitro. This indicates that such a communication may be the functional relevance for the close apposition between MMC and CGRP-IR nerve fibers in vivo.

scholarly journals The unfolding of iRFP713 in a crowded milieu

2018 ◽  
Author(s):  
Olesya V. Stepanenko ◽  
Olga V Stepanenko ◽  
Irina M. Kuznetsova ◽  
Konstantin K Turoverov
Keyword(s):  
Aqueous Solutions ◽  
Molecular Mass ◽  
Intermediate State ◽  
Excluded Volume ◽  
Concentrated Solutions ◽  
Dextran 40 ◽  
Dextran 70 ◽  
Peg 8000 ◽  
Solvent Properties

The exploring of biological processes in vitro under conditions of macromolecular crowding is a way to achieve an understanding of how these processes occur in vivo. In this work, we study the unfolding of the fluorescent probe iRFP713 in crowded environment in vitro. Previously, we showed that the unfolding of the dimeric iRFP713 is accompanied by the formation of a compact monomer and an intermediate state of the protein. In the intermediate state, the macromolecules of iRFP713 have hydrophobic clusters exposed to the surface of the protein and are prone to aggregation. Concentrated solutions of polyethylene glycol (PEG-8000), Dextran-40 and Dextran-70 with a molecular mass of 8000, 40000 and 70000 Da, respectively, were used to model the conditions for macromolecular crowding. A limited available space provided by all the crowding agents used favors to the enhanced aggregation of iRFP713 in the intermediate state at the concentration of guanidine hydrochloride (GdnHCl), at which the charge of protein surface is neutralized by the guanidine cations. This is in line with the theory of the excluded volume. In concentrated solutions of the crowding agents (240–300 mg/ml), the stabilization of the structure of iRFP713 in the intermediate state is observed. PEG-8000 also enhances the stability of iRFP713 in the monomeric compact state, whereas in concentrated solutions of Dextran-40 and Dextran-70 the resistance of the protein in the monomeric state against GdnHCl-induced unfolding decreases. The obtained data argues for the excluded volume effect being not the only factor that contributes the behavior of biological molecules in a crowded milieu. Crowding agents do not affect the structure of the native dimer of iRFP713, which excludes the direct interactions between the target protein and the crowding agents. PEGs of different molecular mass and Dextran-40/Dextran-70 are known to influence the solvent properties of water. The solvent dipolarity/polarizability and basicity/acidity in aqueous solutions of these crowding agents vary in different ways. The change of the solvent properties in aqueous solutions of crowding agents might impact the functioning of a target protein.

Aqueous Solutions as Potential Ultrasonic Contrast Agents

1979 ◽  
Vol 1 (3) ◽  
pp. 265-279 ◽  
Author(s):  
J. Ophir ◽  
R. E. McWhirt ◽  
N. F. Maklad
Keyword(s):  
Aqueous Solutions ◽  
Thermal Effects ◽  
New Approach ◽  
Ultrasonic Properties ◽  
The Past ◽  
Low Toxicity ◽  
Ultrasonic Backscatter ◽  
Sound Density

Enhancement of ultrasonic backscatter and reflectivity from tissues has been demonstrated in the past using gas bubbles and thermal effects. This paper presents a new approach, whereby such enhancement can be achieved by the introduction of suitable aqueous solutions into tissue. Ideally, such solutions should exhibit low toxicity and ultrasonic properties markedly different from those of tissue. Twenty-two potential materials were identified and the speed of sound, density and acoustic impedance in their solutions were determined as a function of concentration. Some of these solutions were used in preliminary in vitro and in vivo canine experiments and echo enhancement was demonstrated.

scholarly journals Small-molecule antibiotic inhibitors of post-translational protein secretion

2020 ◽  
Author(s):  
Mohamed Belal Hamed ◽  
Ewa Burchacka ◽  
Liselotte Angus ◽  
Arnaud Marchand ◽  
Jozefien De Geyter ◽  
...  
Keyword(s):  
Small Molecule ◽  
Bacterial Resistance ◽  
Bacterial Species ◽  
Attractive Potential ◽  
E Coli ◽  
Small Molecule Compound ◽  
Potential Alternative ◽  
Structural Classes

AbstractThe increasing problem of bacterial resistance to antibiotics underscores the urgent need for new antibacterials. The Sec preprotein export pathway is an attractive potential alternative target. It is essential for bacterial viability and includes components that are absent from eukaryotes. Here we used a new high throughput in vivo screen based on the secretion and activity of alkaline phosphatase (PhoA), a Sec-dependent secreted enzyme that becomes active in the periplasm. The assay was optimized for a luminescence-based substrate and was used to screen a ~240K small molecule compound library. After hit confirmation and analoging, fourteen HTS secretion inhibitors (HSI), belonging to 8 structural classes, were identified (IC50 <60 μM). The inhibitors were also evaluated as antibacterials against 19 Gram− and Gram+ bacterial species (including those from the WHO top pathogens list). Seven of them, HSI#6, 9; HSI#1, 5, 10 and HSI#12, 14 representing three structural families were microbicidals. HSI#6 was the most potent (IC50 of 0.4-8.7 μM), against 13 species of both Gram− and Gram+ bacteria. HSI#1, 5, 9 and 10 inhibited viability of Gram+ bacteria with IC50 ~6.9-77.8 μM. HSI#9, 12 and 14 inhibited viability of E. coli strains with IC50 <65 μM. Moreover, HSI#1, 5 and 10 inhibited viability of an E. coli strain missing TolC to improve permeability with IC50 4-14 μM, indicating their inability to penetrate the outer membrane. In vitro assays revealed that antimicrobial activity was not related to inhibition of the SecA component of the translocase and hence HSI molecules may target new unknown components that affect secretion. The results provide proof of principle for our approach, and new starting compounds for optimization.

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