DNA TURNOVER IN BUFFER-HELD ESCHERICHIA COLI AND ITS EFFECT ON REPAIR OF UV DAMAGE

Abstract— Continuous DNA degradation and resynthesis, without a net change in cellular DNA content, were observed in buffer-held, non-irradiated E. coli B/r. This constant DNA turnover probably involves most of the genome and reflects random sites of DNA repair due to the polA-dependent excision-resynthesis repair pathway. Under these non-growth conditions, it appears that at any given time there is a minimum of one repair site per 6.5 × 10⁶ daltons DNA, each of which is at least 160 nucleotides long.
While the amount of DNA degradation is not influenced by prior exposure to UV radiation, the synthetic activity decreases with increasing UV fluence. We suggest that when sites of DNA turnover occur opposite to cyclobutyl dipyrimidines in UV-irradiated cells, repair of the latter damage can be prevented. This implies that both beneficial and deleterious processes take place in irradiated buffer-held cells, and that cell survival depends on the delicate balance between DNA turnover and repair of UV-damage. Based on these findings, we propose a model to explain the limited repair observed during post-irradiation liquid-holding and to account for the large difference in cell survival between irradiation at low fluence rates (fluence-rate dependent recovery) and at high fluence rates followed by liquid-holding (liquid-holding recovery).     

Collective Effects in Ionic Liquid [emim][Tf2N] and Ionic Paramagnetic Nitrate Solutions without Long-Range Structuring

Mesoscopic shear elasticity has been revealed in ordinary liquids both experimentally by reinforcing the liquid/surface interfacial energy and theoretically by nonextensive models. The elastic effects are here examined in the frame of small molecules with strong electrostatic interactions such as room temperature ionic liquids [emim][Tf2N] and nitrate solutions exhibiting paramagnetic properties. We first show that these charged fluids also exhibit a nonzero low-frequency shear elasticity at the submillimeter scale, highlighting their resistance to shear stress. A neutron scattering study completes the dynamic mechanical analysis of the paramagnetic nitrate solution, evidencing that the magnetic properties do not induce the formation of a structure in the solution. We conclude that the elastic correlations contained in liquids usually considered as viscous away from any phase transition contribute in an effective way to collective effects under external stress whether mechanical or magnetic fields.     

Food Peptides,Gut Microbiota Modulation,and Antihypertensive Effects

The gut microbiota is increasingly important in the overall human health and as such, it is a target in the search of novel strategies for the management of metabolic disorders including blood pressure, and cardiovascular diseases. The link between microbiota and hypertension is complex and this review is intended to provide an overview of the mechanism including the production of postbiotics, mitigation of inflammation, and the integration of food biological molecules within this complex system. The focus is on hydrolyzed food proteins and peptides which are less commonly investigated for prebiotic properties. The analysis of available data showed that food peptides are multifunctional and can prevent gut dysbiosis by positively affecting the production of postbiotics or gut metabolites (short-chain fatty acids, polysaccharides, biogenic amines, bile acids). Peptides and the postbiotics then displayed antihypertensive effects via the renin-angiotensin system, the gut barrier, the endothelium, and reduction in inflammation and oxidative stress. Despite the promising antihypertensive effect of the food peptides via the modulation of the gut, there is a lack of human studies as most of the works have been conducted in animal models.     

On the Effect of the Various Assumptions and Approximations used in Molecular Simulations on the Properties of Bio-Molecular Systems: Overview and Perspective on Issues

Computer simulations of molecular systems enable structure-energy-function relationships of molecular processes to be described at the sub-atomic, atomic, supra-atomic or supra-molecular level and plays an increasingly important role in chemistry, biology and physics. To interpret the results of such simulations appropriately, the degree of uncertainty and potential errors affecting the calculated properties must be considered. Uncertainty and errors arise from (1) assumptions underlying the molecular model, force field and simulation algorithms, (2) approximations implicit in the interatomic interaction function (force field), or when integrating the equations of motion, (3) the chosen values of the parameters that determine the accuracy of the approximations used, and (4) the nature of the system and the property of interest. In this overview, advantages and shortcomings of assumptions and approximations commonly used when simulating bio-molecular systems are considered. What the developers of bio-molecular force fields and simulation software can do to facilitate and broaden research involving bio-molecular simulations is also discussed.     

The Prospect of Dimensionality in Porous Semiconductors

With the advent of silicon-based semiconductors, a plethora of previously unknown technologies became possible. The development of lightweight low-dimensional organic semiconductors followed soon after. However, the efficient charge/electron transfers enabled by the non-porous 3D structure of silicon is rather challenging to be realized by their (metal-)organic counterparts. Nevertheless, the demand for lighter, more efficient semiconductors is steadily increasing resulting in a growing interest in (metal-)organic semiconductors. These novel materials are faced with a variety of challenges originating from their chemical design, their packing and crystallinity. Although the effect of molecular design is quite well understood, the influence of dimensionality and the associated change in properties (porosity, packing, conjugation) is still an uncharted area in (metal-)organic semiconductors, yet highly important for their practical utilization. In this Minireview, an overview on the design and synthesis of porous semiconductors, with a particular emphasis on organic semiconductors, is presented and the influence of dimensionality is discussed.     

Fast and Reliable Automated Synthesis of RNA and Partially 2′-O- Protected Precursors (`Caged RNA') Based on Two Novel,Orthogonal 2′-O-Protecting Groups,Preliminary Communication

Two sets of RNA phosphoramidites, carrying the (fluoride-labile) 2′-O-[(triisopropylsilyl)oxy]methyl (=tom) group and the (photolabile) [(R)-1-(2-nitrophenyl)ethoxy]methyl (=(R)-npeom) group, were prepared (see 1 – 4 and 5 – 8 , resp.). The two protecting groups were completely orthogonal to each other. Three ribozyme-substrate constructs, protected each by a (R)-npeom group, were synthesized; on photolysis, efficient cleavage of this remaining protecting group occurred (Scheme 3). It could be demonstrated that the presence of one (R)-npeom group within a RNA strand has only a minor influence on the pairing properties of corresponding duplexes.     

Scanning electrochemical microscopy as a probe of Ag+ binding kinetics at Langmuir phospholipid monolayers

A new method has been developed for measuring local adsorption rates of metal ions at interfaces based on scanning electrochemical microscopy (SECM). The technique is illustrated with the example of Ag+ binding at Langmuir phospholipid monolayers formed at the water/air interface. Specifically, an inverted 25 microm diameter silver disc ultramicroelectrode (UME) was positioned in the subphase of a Langmuir trough, close to a dipalmitoyl phosphatidic acid (DPPA) monolayer, and used to generate Ag+ via Ag electro-oxidation. The method involved measuring the transient current-time response at the UME when the electrode was switched to a potential to electrogenerate Ag+. Since the Ag+/Ag couple is reversible, the response is highly sensitive to local mass transfer of Ag+ away from the electrode, which, in turn, is governed by the interaction of Ag+ with the monolayer. The methodology has been used to determine the influence of surface pressure on the adsorption of Ag+ ions at a phospholipid (dipalmitoyl phosphatidic acid) Langmuir monolayer. It is shown that the capacity for metal ion adsorption at the monolayer increased as the density of surface adsorption sites increased (by increasing the surface pressure). A model for mass transport and adsorption in this geometry has been developed to explain and characterise the adsorption process.     

Molecular recognition in a uradinyl-functionalized stable radical

Stable radical 2-(6-uradinyl)-4,4,5,5-tetramethyl-4,5-dihydro-1H-imidazole-1-oxyl (1) binds to hydrogen-bonding complement 2,6-di(propylamido)pyridine (DAP) in chloroform with Ka=220 M(-1) at 33 degrees C; ESI-MS shows not only 1:DAP complementary dyad formation, but also 1:(DAP)2 formation at higher concentrations of DAP.     

Electrochemical templating of metal nanoparticles and nanowires on single-walled carbon nanotube networks

The use of single-walled carbon nanotube (SWNT) networks as templates for the electrodeposition of metal (Ag and Pt) nanostructures is described. Pristine SWNTs, grown on insulating SiO2 surfaces using catalyzed chemical vapor deposition, served as the working electrode. In the simplest case, electrical contact was made by depositing a gold strip on the SWNT substrate (device 1). Deposition of Ag and Pt over extensive periods (30 s) resulted in a high density of particles on the SWNTs, with almost contiguous nanowire formation from the Au/SWNT boundary moving to isolated nanoparticles at further distances from the contact. For direct electrochemical studies of Ag and Pt nucleation, the assembly was coated in a resist layer and a small window opened up to expose only the electrically connected SWNTs to solution (device 2). In this case, the electrochemical signature in voltammetric and amperometric studies of metal deposition was due solely to processes at the SWNTs. Coupled with high-resolution microscopy measurements (atomic force microscopy and field emission scanning electron microscopy), this approach provided detail on the nucleation and growth mechanisms of Ag and Pt on SWNTs under electrochemical control. In particular, Ag growth was found to be rapid and progressive with an increasing nanoparticle density with time, whereas Pt deposition was characterized by lower nucleation densities and slower growth rates with a tendency for larger particles to be produced over long times.     

Harmonization and transferability of performance assessment: experience from four serum aluminum proficiency testing schemes

Proficiency testing schemes monitor laboratory performance and provide a stimulus for improvement in accuracy. Where several schemes operate in the same analytical sector, there are risks that assessments of performance may be in conflict. Performance assessment for the determination of trace elements such as aluminum in serum is particularly important due to the high risk of contamination and therefore erroneous results. The objectives of this work were (1) to compare several mathematical models to establish a predefined standard deviation for proficiency assessment and (2) to evaluate the influence of instrumental methods and proficiency testing scheme on the assessment of performance for serum aluminum measurements. For this purpose, three samples were sent to the participants of four proficiency testing schemes. Assigned values were calculated according to algorithm A according to ISO 13528 and standard deviation for proficiency assessment according to three methods based on individual variability, state of the art or previous proficiency testing results. The method based on individual variability produced a more stringent standard deviation compared to analytical imprecision based on the state of the art. The instrumental methods gave similar results, whereas significant differences were observed between the four proficiency testing schemes indicating that harmonization of the standard deviation for proficiency assessment fails to allow transferability from one proficiency testing scheme to another and that additional factor(s) contribute to variability in performance assessment.