On the biophysics of cathodal galvanotaxis in rat prostate cancer cells: Poisson-Nernst-Planck equation approach

Rat prostate cancer cells have been previously investigated using two cell lines: a highly metastatic one (Mat-Ly-Lu) and a nonmetastatic one (AT-2). It turns out that the highly metastatic Mat-Ly-Lu cells exhibit a phenomenon of cathodal galvanotaxis in an electric field which can be blocked by interrupting the voltage-gated sodium channel (VGSC) activity. The VGSC activity is postulated to be characteristic for metastatic cells and seems to be a reasonable driving force for motile behavior. However, the classical theory of cellular motion depends on calcium ions rather than sodium ions. The current research provides a theoretical connection between cellular sodium inflow and cathodal galvanotaxis of Mat-Ly-Lu cells. Electrical repulsion of intracellular calcium ions by entering sodium ions is proposed after depolarization starting from the cathodal side. The disturbance in the calcium distribution may then drive actin polymerization and myosin contraction. The presented modeling is done within a continuous one-dimensional Poisson-Nernst-Planck equation framework.     

Exposure to humans and activity pattern of European souslik (Spermophilus citellus) in zoo conditions

European souslik (Spermophilus citellus) is an endangered species being the subject of reintroduction plan in some European countries, including Poland. It is important to obtain data about behavior of reintroduced species, especially a reaction to captivity of specimens prepared to release. The aim of this study was to evaluate influence of human exposure on sousliks behavior. Observed animals were kept in Poznań zoo in three enclosures. Two of them (called "high noise") were in part of the zoo available to the visitors, whereas one ("low noise") was in part closed for them. In "high noise" enclosures sousliks spent more time outside burrows and more specimens were present above ground. They also ate and ran more frequently in "high noise" enclosure, whereas emitted loud voices more often in the "low noise" one. In all enclosures more animals were present above grounds in absence of humans. Time spent by one souslik above ground was positively significantly correlated with the number of sousliks outside burrows. European sousliks observed in this study were used to humans and were less vigilant if they were exposed to permanent humans presence, but they did not become tamed and behave in a way similar to free living animals.     

Weighted least-squares likelihood ratio test for branch testing in phylogenies reconstructed from distance measures

A variety of analytical methods is available for branch testing in distance-based phylogenies. However, these methods are rarely used, possibly because the estimation of some of their statistics, especially the covariances, is not always feasible. We show that these difficulties can be overcome if some simplifying assumptions are made, namely distance independence. The weighted least-squares likelihood ratio test (WLS-LRT) we propose is easy to perform, using only the distances and some of their associated variances. If no variances are known, the use of the Felsenstein F-test, also based on weighted least squares, is discussed. Using simulated data and a data set of 43 mammalian mitochondrial sequences we demonstrate that the WLS-LRT performs as well as the generalized least-squares test, and indeed better for a large number of taxa data set. We thus show that the assumption of independence does not negatively affect the reliability or the accuracy of the least-squares approach. The results of the WLS-LRT are no worse than the results of the bootstrap methods, such as the Felsenstein bootstrap selection probability test and the Dopazo test. We also show that WLS-LRT can be applied in instances where other analytical methods are inappropriate. This point is illustrated by analyzing the relationships between human immunodeficiency virus type 1 (HIV-1) sequences isolated from various organs of different individuals.     

Xanthine, xanthosine and its nucleotides: solution structures of neutral and ionic forms, and relevance to substrate properties in various enzyme systems and metabolic pathways

The 6-oxopurine xanthine (Xan, neutral form 2,6-diketopurine) differs from the corresponding 6-oxopurines guanine (Gua) and hypoxanthine (Hyp) in that, at physiological pH, it consists of a approximately 1:1 equilibrium mixture of the neutral and monoanionic forms, the latter due to ionization of N(3)-H, in striking contrast to dissociation of the N(1)-H in both Gua and Hyp at higher pH. In xanthosine (Xao) and its nucleotides the xanthine ring is predominantly, or exclusively, a similar monoanion at physiological pH. The foregoing has, somewhat surprisingly, been widely overlooked in studies on the properties of these compounds in various enzyme systems and metabolic pathways, including, amongst others, xanthine oxidase, purine phosphoribosyltransferases, IMP dehydrogenases, purine nucleoside phosphorylases, nucleoside hydrolases, the enzymes involved in the biosynthesis of caffeine, the development of xanthine nucleotide-directed G proteins, the pharmacological properties of alkylxanthines. We here review the acid/base properties of xanthine, its nucleosides and nucleotides, their N-alkyl derivatives and other analogues, and their relevance to studies on the foregoing. Included also is a survey of the pH-dependent helical forms of polyxanthylic acid, poly(X), its ability to form helical complexes with a broad range of other synthetic homopolynucleotides, the base pairing properties of xanthine in synthetic oligonucleotides, and in damaged DNA, as well as enzymes involved in circumventing the existence of xanthine in natural DNA.     

Regulation of transcription of katE and katF in Escherichia coli

Fusion plasmids with lacZ under the control of the katE (encoding catalase or hydroperoxidase HPII) and katF (encoding a sigma factor-like protein required for katE expression) promoters were constructed. Expression from both katE and katF promoters was low in rich medium but elevated in poor medium during log-phase growth. Furthermore, the slowdown in growth as cells entered the stationary phase in rich medium, a result of carbon source depletion, was associated with an increase in katE and katF expression. A simple reduction in the carbon source level as the cells entered the stationary phase was not responsible for the increase in expression, because transferring the culture to a medium with no glucose did not induce expression from either promoter. Spent rich medium from stationary-phase cells was capable of inducing expression, as were simple aromatic acids such as benzoate, o-hydroxybenzoate, and p-aminobenzoate added to new medium. Anaerobiosis did not cause an increase in expression, nor did it significantly change the pattern of expression. Regardless of the medium, katF expression was always turned on before or coincidently with katE expression; in the presence of benzoate katF was fully induced, whereas katE was only partially induced, suggesting that a factor in addition to KatF protein was involved in katE expression. During prolonged aerobic incubation, cells lacking katF died off more rapidly than did cells lacking either katE or katG.     

Interpretation of fluorescence decay kinetics in 3-methylbenzimidazolyl(5′-5′)guanosine dinucleotides: exponential dependence on the number of phosphates in the polyphosphate bridge

The number of phosphate groups in the 5′,5′-polyphosphate bridge of mRNA-cap dinucleotide analogues affects kinetics of long-range electron transfer (ET) responsible for 3-methylbenzimidazole (m³B) fluorescence quenching in model dinucleotides. For instance, 3-methylbenzimidazolyl(5′-5′)guanosine dinucleotides (m³Bp _n G, n = 2, 3, 4) having m³B donor, 5′-5′ polyphosphate bridge, and guanine (G) acceptor, exhibit exponential dependence of the ET rate on the number of phosphates, i.e. donor–acceptor distance. Involvement of the 5′-5′ polyphosphate bridge in the ET is strongly indicated by lack of m³B-G stacking effect on the exponential factor, which is the same at 20°C, where m³B-G intramolecular stacking dominates, as that at 75°C where stacking–unstacking equilibrium is shifted in favour of the unstacked structure.     

Ab initio multireference study of Hetero-Diels-Alder reaction of buta-1,3-diene with alkyl glyoxylates

Hetero-Diels-Alder (HDA) reaction of methyl glyoxylate with buta-1,3-diene has been investigated using multireference methods (complete active space SCF and multi-reference perturbation theory) and compared with several single-reference methods (including DFT) often used in calculations of catalysed [4+2] cycloadditions. Concerted and stepwise mechanisms, found in the literature, are compared. It is shown, that the stepwise mechanism may be a result of choosing unbalanced active space. Such choice leads to very close singlet and triplet states in the intermediate geometry - an artificial effect, that disappears if properly balanced active space is used (here, we use active space of 12 orbitals and 12 electrons). Conclusions concerning the mechanism and usefulness of the applied methodology are drawn, which might be important for theoretical investigation of stereoselectivity and specificity of catalysts for the HDA reaction. Figure Hetero-Diels-Alder reaction of alkyl glyoxylates with buta-1,3-diene, investigated using multi- and single-reference ab initio methods Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.