The role of antioxidant systems in the response of Escherichia coli to acetamidophenol and some antibiotics

The role of glutathione and other antioxidant systems in the response of Escherichia coli to acetamidophenol (paracetamol), rifampicin, and chloramphenicol was studied. The exposure of aerobically growing E. coli cells to acetamidophenol diminished the intracellular level of glutathione by 40% and the reduced-to-oxidized glutathione ratio in the cells by 50%, while it enhanced the expression of the antioxidant genes soxS and sodA by 2.7 and 1.8 times, respectively. Glutathione-deficient cells were more susceptible to acetamidophenol than were normal cells. All this suggests that acetamidophenol induces a mild oxidative stress in E. coli cells. The oxidative stress induced by rifampicin was still less pronounced, whereas chloramphenicol-treated E.coli cells exhibited no signs of oxidative stress at all.     

Impact of Temperature Dependent Sampling Procedures in Proteomics and Peptidomics – A Characterization of the Liver and Pancreas Post Mortem Degradome

Little is known about the nature of post mortem degradation of proteins and peptides on a global level, the so-called degradome. This is especially true for nonneural tissues. Degradome properties in relation to sampling procedures on different tissues are of great importance for the studies of, for instance, post translational modifications and/or the establishment of clinical biobanks. Here, snap freezing of fresh (<2 min post mortem time) mouse liver and pancreas tissue is compared with rapid heat stabilization with regard to effects on the proteome (using two-dimensional differential in-gel electrophoresis) and peptidome (using label free liquid chromatography). We report several proteins and peptides that exhibit heightened degradation sensitivity, for instance superoxide dismutase in liver, and peptidyl-prolyl cis-trans isomerase and insulin C-peptides in pancreas. Tissue sampling based on snap freezing produces a greater amount of degradation products and lower levels of endogenous peptides than rapid heat stabilization. We also demonstrate that solely snap freezing related degradation can be attenuated by subsequent heat stabilization. We conclude that tissue sampling involving a rapid heat stabilization step is preferable to freezing with regard to proteomic and peptidomic sample quality.The evolving maturation of the field of proteomics has, in the same way as in genomics, highlighted the need of better sampling procedures and sample preparation methodologies to minimize the effect of post mortem alterations. The aspect of sample quality is not new in any way and is relevant in most biomedical fields but has only lately started to receive adequate attention. The main factors influencing sample quality is storage temperature of the body until tissue removal (foremost a problem in clinical settings and extraction of less accessible tissue samples from model organisms) and post mortem interval (PMI)¹ (1–3). Post mortem degradation in during PMI is a well known compromising problem when studying endogenous peptides (2, 3) and has also been proven to affect the results of polypeptide (here defined as proteins larger than 10 kDa) studies (3–8). PMI degradation has mainly been studied on human or mouse brain tissue, using two-dimensional electrophoresis (2-DE), SDS-PAGE, and immunoblotting (1, 3–12). There are also a few proteomic studies on muscle tissue degradation in livestock (13–16).We and others have previously explored the effect of focused microwave irradiation with regard to sample quality, demonstrating that this method is more reliable than snap freezing in liquid nitrogen, especially with regard to post-translational modification (PTM) stability (2, 3, 17–20). An alternative method based on cryostat dissection with subsequent heat treatment through boiling has also been reported to improve endogenous peptide sample quality (21). Besides focused microwave irradiation, which is specifically used for rodent brain tissue sampling, we have also demonstrated the efficiency of rapid heat stabilization through conductivity with regard to sample degradation (3, 22). Although somewhat constrained by its dependence on how quickly the tissue is harvested from the body, the latter procedure has the added advantage that it can be used on any type of tissue and species, fresh as well as frozen. This study will compare effects of sampling procedures on the liver and pancreas degradome following rapid heat stabilization, the more traditional snap freezing, or the combination of snap freezing with subsequent heat stabilization.To summarize, this study investigated the effects of post mortem degradation in pancreas and liver. Both tissues are well studied because of their multiple functions in the body and their involvement in different diseases such as diabetes or hepatocarcinoma. Pancreas is especially interesting in this context as it displays endocrine secretion of peptides, and exocrine secretion of digestive enzymes, the later making it a protease rich tissue. We used both two-dimensional difference in gel electrophoresis (2D-DIGE) and label free liquid chromatography mass spectrometry (LC-MS) based differential peptide display (2, 18), the later to better investigate changes in small molecular fragment that are not easily detectable by gel-based methods. 2D-DIGE is an unrivaled methodology to characterize alterations in isoform patterns, which is an important aspect considering that post-translational modifications (PTMs) such as phosphorylations are especially sensitive to post mortem influence within a few minutes PMI (3). The peptidomics approach has been used in several studies to point out early post mortem changes and protein degradation that tissue undergo following sampling and is therefore a well-suited method (3, 18, 22).     

Orienting reflex: "targeting reaction" and "searchlight of attention"

The concept of orienting reflex based on the principle of vector coding of cognitive and executive processes is proposed. The orienting reflex to non-signal and signal stimuli is a set of orienting reactions: motor, autonomic, neuronal, and subjective emphasizing new and significant stimuli. Two basic mechanisms can be identified within the orienting reflex: a "targeting reaction" and a "searchlight of attention". In the visual system the first one consists in a foveation of a target stimulus. The foveation is performed with participation of premotor neurons excited by saccadic command neurons of the superior colliculi. The "searchlight of attention" is based on the resonance of gamma-oscillations in the reticular thalamus selectively enhancing responses of cortical neurons (involuntary attention). The novelty signal is generated in novelty neurons of the hippocampus, which are selectively tuned to a repeatedly presented standard stimulus. The selective tuning is caused by the depression of plastic synapses representing a "neuronal model" of the standard stimulus. A mismatch of the novel stimulus with the established neuronal model gives rise to a "novelty signal" enhancing the novel input. The novelty signal inhibits current conditioned reflexes (external inhibition) contributing to redirecting the behavior. By triggering the expression of early genes the novelty signal initiates the formation of the long-term memory connected with neoneurogenesis.     

Russian genofond. Genogeography of surnames

Surnames are traditionally used in population genetics as "quasi-genetic" markers (i.e., analogs of genes) when studying the structure of the gene pool and the factors of its microevolution. In this study, spatial variation of Russian surnames was analyzed with the use of computer-based gene geography. Gene geography of surnames was demonstrated to be promising for population studies on the total Russian gene pool. Frequencies of surnames were studied in 64 sel'sovets (rural communities; a total of 33 thousand persons) of 52 raions (districts) of 22 oblasts (regions) of the European part of Russia. For each of 75 widespread surnames, an electronic map of its frequency was constructed. Summary maps of principal components were drawn based on all maps of individual surnames. The first 5 of 75 principal components accounted for half of the total variance, which indicates high resolving power of surnames. The map of the first principal component exhibits a trend directed from the northwestern to the eastern regions of the area studied. The trend of the second component was directed from the southwestern to the northern regions of the area studied, i.e., it was close to latitudinal. This trend almost coincided with the latitudinal trend of principal components for three sets of data (genetic, anthropological, and dermatoglyphical). Therefore, the latitudinal trend may be considered the main direction of variation of the Russian gene pool. The similarity between the main scenarios for the genetic and quasi-genetic markers demonstrates the effectiveness of the use of surnames for analysis of the Russian gene pool. In view of the dispute between R. Sokal and L.L. Cavalli-Sforza about the effects of false correlations, the maps of principal components of Russian surnames were constructed by two methods: through analysis of maps and through direct analysis of original data on the frequencies of surnames. An almost complete coincidence of these maps (correlation coefficient rho = 0.96) indicates that, taking into account the reliability of the data, the resultant maps of principal components have no errors of false correlations.     

Determination of the parameters for producing a biobinder from wood: a mathematical modeling of the transformation of lignocellulose substrate by the fungus Panus tigrinus

A biochemical scheme for the transformation of wood lignocellulose during enzymatic hydrolysis of polysaccharides and lignin destruction in reactions involving free radicals was developed, and a corresponding mathematical model was constructed. Processing (fermentation) of wood particles by the fungus Panus tigrinus in a submerged culture for producing a biobinder of wood composites--woodchip boards and fiber-boards--is considered. The mathematical model was used to study the technological parameters that influence the production of enzymes and fungal biomass and the level of free radical accumulation in the substrate, i.e., the factors determining the production of the biobinder. The optimal values of these parameters were determined, namely: the specific surface of wood particles, amounting to 2000 cm2/g; processing time of 56 h; and an initial concentration of 3.0 g/l of fungal biomass in the submerged culture.     

Profiles of the utilization of 20 amino acids as the only source of nitrogen and carbon in bacteria of the genera Klebsiella, Enterobacter, Serratia, Escherichia

The profiles of the utilization of 20 protein amino acids in 118 Klebsiella pneumoniae sub- sp. pneumoniae, K. oxytoca, K. planticola, K. mobilis, Enterobacter cloacae, Serratia marscescens, S. liquefaciens, Escherichia coli strains isolated from clinical material were studied. The utilization of amino acids was determined on minimal saline agar containing amino acid as the only source of nitrogen and carbon; the results were evaluated after 72-hour incubation at 37 degrees C. 17 profiles of amino-acid utilization were thus determined, most of them genus-specific in enterobacteria: Klebsiella (profiles No. 1--6, 9, 10), Enterobacter (No. 11--13), Serratia (No. 14--16), Escherichia (No. 17). The full coincidence of amino-acid utilization profiles in bacteria of K. mobilis (No. 1, 6) and K. pneumoniae subsp. pneumoniae with out of such profiles in bacteria of the genera Enterobacter, Serratia, Escherichia was established, which confirmed that K. mobilis (formerly Enterobacter aerogenes) belonged to the genus Klebsiella.     

Identification of Ca(2+)-activated Mg(2+)-dependent ATP-hydrolase activity of membrane microsomal fraction of loach embryo (Misgurnus fossilis L.)

The functional confirmation of availability of Ca2+ transport initially-active systems in the embryo cells of loach Misgurnus fossilis L. has been obtained. Using thapsigargin, the specific inhibitor of endoplasmic reticulum of Ca2+, Mg(2+)-ATPase, this enzyme activity was divided into thapsigargin-sensitive (actually endoplasmic reticulum Ca2+, Mg(2+)-ATPase) and thapsigargin-insensitive (plasma membrane Ca2+, Mg(2+)-ATPase) constituents. The Ca(2+)-independent Mg(2+)-dependent ATPase activity makes above 39.7% of the common Ca2+, Mg(2+)-ATPase activity of embryo loach. The periodic changes of Ca2+, Mg(2+)-ATPase activity (except for the changes of plasma membrane Ca2+, Mg(2+)-ATPase activity) were found out, which coincide with periodic [Ca2+]i oscillations during the synchronous divisions of loach blastomers embryos.