Simulations of action of DNA topoisomerases to investigate boundaries and shapes of spaces of knots

The configuration space available to randomly cyclized polymers is divided into subspaces accessible to individual knot types. A phantom chain utilized in numerical simulations of polymers can explore all subspaces, whereas a real closed chain forming a figure-of-eight knot, for example, is confined to a subspace corresponding to this knot type only. One can conceptually compare the assembly of configuration spaces of various knot types to a complex foam where individual cells delimit the configuration space available to a given knot type. Neighboring cells in the foam harbor knots that can be converted into each other by just one intersegmental passage. Such a segment-segment passage occurring at the level of knotted configurations corresponds to a passage through the interface between neighboring cells in the foamy knot space. Using a DNA topoisomerase-inspired simulation approach we characterize here the effective interface area between neighboring knot spaces as well as the surface-to-volume ratio of individual knot spaces. These results provide a reference system required for better understanding mechanisms of action of various DNA topoisomerases.     

Shapes of curves of pH-dependence of reactions

A simple case is considered in which the rate of a two-step reaction depends on pH because the intermediate formed in the first step has to gain (or lose) a proton before it can react in the second step, and in which the rate-determining step therefore changes with pH. The curves of reaction rate against pH are shown to be symmetrical, and the sharpest peak possible has a width at half its height of 1.53pH units, i.e. of 2log(3+2 radical2). Any particular curve for this situation proves to be identical with a curve that could be generated for the pH-dependence of a single-step reaction in which the rate is proportional to the concentration of a particular ionic form of a reactant. Curves for the latter situation, however, can have forms impossible for the former case in which the rate-determining step changes, but only if the protonations that activate and deactivate the reactant are co-operative. The peak can then become even sharper, and its width at half its height can fall to 1.14pH units, i.e. to 2log(2+ radical3).     

Isolation of domains of the plasma membrane of hepatocytes

Several recent studies have demonstrated the ability of techniques based on immunoadsorption to selectively isolate specialized subregions of membranes, termed domains, which are derived from a larger more complex parent membrane like the plasma membrane. The immunoadsorbent is directed against a specific antigen that resides exclusively or predominantly in the membrane domain to be isolated. Thus, a monospecific antibody to the domain-specific antigen is required. In the present study we developed a method employing a modified immunoblotting strategy which could utilize polyspecific antibodies to isolate membrane vesicles derived from a specific membrane domain of the hepatocyte plasma membrane. We also used specific cell surface labeling of the hepatocyte plasma membrane by lactoperoxidase-catalyzed iodination at 4 degrees C and preparation of different sized vesicles by sonication to facilitate isolation of the specific domain. For this study, polyspecific antisera were raised in goats against a membrane fraction, denoted N2u, which is enriched in bile canalicular proteins. This antiserum recognizes, among other antigens, a 110,000 Mr polypeptide previously shown to be localized in the bile canaliculus (J. Cook et al. (1983) J. Cell. Biol. 97, 1823-1833). A monospecific antiserum was raised in rabbits against the rat hepatocyte asialoglycoprotein receptor, a sinusoidal domain-specific set of glycoproteins whose major form has a Mr of 43,000. These antisera were each coupled indirectly to different pieces of nitrocellulose by the immunoblotting protocol and were used to isolate membrane vesicles from a crude extract of liver plasma membrane prepared by sonication. The ratio of iodinated asialoglycoprotein receptor to the 110,000 Mr polypeptide in vesicles isolated by the affinity nitrocellulose immunoadsorbent method indicate a 10- to 15-fold enrichment of sinusoidal-derived vesicles relative to bile canalicular-derived membrane vesicles. These results show that the affinity nitrocellulose immunoadsorbent method can be used to isolate domain-specific vesicles. Further, the affinity immunoadsorbent method described here for the isolation of domains of the plasma membrane is an integrative one allowing isolation of vesicles present in relatively small concentration in crude cell extracts and it requires minimal ultracentrifugation time.     

The Effect of Conflicting Pressures on the Evolution of Division of Labor

Within nature, many groups exhibit division of labor. Individuals in these groups are under seemingly antagonistic pressures to perform the task most directly beneficial to themselves and to potentially perform a less desirable task to ensure the success of the group. Performing experiments to study how these pressures interact in an evolutionary context is challenging with organic systems because of long generation times and difficulties related to group propagation and fine-grained control of within-group and between-group pressures. Here, we use groups of digital organisms (i.e., self-replicating computer programs) to explore how populations respond to antagonistic multilevel selection pressures. Specifically, we impose a within-group pressure to perform a highly-rewarded role and a between-group pressure to perform a diverse suite of roles. Thus, individuals specializing on highly-rewarded roles will have a within-group advantage, but groups of such specialists have a between-group disadvantage. We find that digital groups could evolve to be either single-lineage or multi-lineage, depending on experimental parameters. These group compositions are reminiscent of different kinds of major evolutionary transitions that occur within nature, where either relatives divide labor (fraternal transitions) or multiple different organisms coordinate activities to form a higher-level individual (egalitarian transitions). Regardless of group composition, organisms embraced phenotypic plasticity as a means for genetically similar individuals to perform different roles. Additionally, in multi-lineage groups, organisms from lineages performing highly-rewarded roles also employed reproductive restraint to ensure successful coexistence with organisms from other lineages.     

Application of the function of the number of states of dynamic system to investigation of electroencephalographic reaction to photostimulation

A new way of EEG analysis is developed, which makes it possible to reveal a reaction of the brain cortex to external stimulation at a low response level. The method is based on the creation of an image of the EEG curve in the discrete phase space and comparison of a current condition with the conditions from a certain basic set. The strength of reaction to external stimulation is defined by the incidence of conditions novel with respect to the basic ones.     

Thermostability of Proteases and Lipases from a Number of Species of Psychrotrophic Bacteria of Dairy Origin

Proteases and lipases from a number of different species of psychrotrophic bacteria isolated from dairy products are resistant to heat treatments of 77°C for a holding time of 17 s and 140°C for a holding time of 5s. A further treatment combining the 77°C for 17 s heating process with a heat treatment involving a temperature of 55°C for 1 h was also examined. The proteases and, to a lesser extent, the lipases were also resistant to the treatments in combination. The resistance of proteases and lipases to inactivation by a treatment of 55°C for 1 h varied between and within species. Therefore, this treatment may not have a widespread practical application.     

An analysis of non-bonded energy of proteins

Non-bonded energy of 16 proteins was calculated using the atomic co-ordinates obtained by X-ray crystallography. The curve of total energy against the number of atoms in proteins is approximately linear with a slight concaved shape. According to a linear equation to fit the curve, the extrapolated length of a polypeptide chain of a globular shape is expected to be 18 residues, which corresponds conceivably to an approximate size of nucleus for a folding of the polypeptide chain. Contributions from short-range and medium-range energies are always much greater than those from long-range energy for all the proteins and there seems to exist a change of each contribution in a range from 1200 to 1700 atoms. The energies with a lag less than four residues are a major part of the total energy and the contribution of energy from main-chain atoms is considerably higher than that from side-chain atoms. Side-chain atoms of a residue have a tendency to interact more strongly with main-chain atoms of N-terminal, than with those of C-terminal side of the residue, indicating asymmetry of the interaction in a protein. Amino acid residues in proteins may be divided into three groups by the order of strength of average energy. The first group exhibiting strong interaction consists mainly of hydrophobic amino acids and the third group consists of hydrophilic ones corresponding to the location in a protein molecule. Cys, val, leu and met are important for medium-range and long-range energies; gly and ala for medium-range energy; ile, trp, phe, tyr and arg for long-range energy. One simple application of the average energy of amino acid residues is illustrated to estimate local energy of a segment of nine residues given by a protein sequence. There is a good correlation between the curve computed by the average energy and the experimental curve for myoglobin.     

Measurement of three-dimensional structure of plants with a simple device and estimation of light capture of individual leaves

1. A simple device called a 'pocometer' (POlar COordinate METER) was developed to measure three-dimensional structure of plants. It consists of a tape-measure to measure distance and two protractors to measure zenith angle and azimuth angle.
2. The pocometer can determine locations of points within a few metres distance with a resolution of less than 1cm. Location of any point on a plant can be measured in 10 to 30s depending on the ease of pulling the tape measure to the point of interest.
3. A system to use data obtained with the pocometer to calculate plant light capture was developed. The degree of shading at any point on a plant is estimated by checking obstruction by other plant parts of the view toward the sky at that point.
4. Photon flux density (PFD) on leaf surfaces was estimated for Aucuba japonica , a broad-leaved evergreen shrub, using the above system. The estimated PFDs for individual leaves of a plant corresponded to the sensor-measured PFDs with correlation coefficients of 0·67 to 0·92.     

Findings of the importance of dietetic fiber in the regulation of cholesterolemia

We studied the variations of some lipid indexes in cholesterolemia, lipidemia and triglycerides in relation to a diet rich in bulk. Seven adult male subjects in good health were tested for cholesterol, lipid and triglycerides before and after a two week period of a dialy diet of 40 g of whole wheat bran containing about 10g of fiber. At the some time the lipid, cholesterol and triglycerides limits were measured in 3 groups of rabbits. The first groups was subjected to a normal diet, the second group was subjected to a diet of bleached flour and vitamins, and the third group had a diet similar to the second group but with the addition of 40 g whole wheat bran. The results of our investigation demonstrated a statistically significant decrease of cholesterol lipid and triglycerides levels the special diets at the some time we did not see in increase in the third group of rabbit. Our study seems to indicate that dietetic fibers exercise a vital role in regulating the concentration of plasma lipids even if the subject continues to consume a diet rich in fats. From this we see to importance of the dietetic fibers as a protective factor in the prevention of ateriosclerotic.     

Characteristics of crossed resistance of neoplastic cells with high level of colchicine resistance

Using a long-term selection the authors obtained the cells of a hamster with a rather high level of stability to colchicine (800-16,600 times). The nature of resistance of these cells to actinomycin differed from those having general origin with the newly obtained but having a lower level of stability to colchicine. This level of stability did not correlate with that to a selective agent.     

Formulation of Statistical Equation of Motion of Blood

A general form of the statistical equation of motion of the blood is derived by averaging the motion of individual elements of the blood over a small volume in space. This equation can be transformed into an explicit form to find the constitutive equations of the blood provided the detailed motion of the plasma in some neighborhood of a suspended particle is known. As a demonstration of such transformation, the general form of the statistical equation of motion is applied to the suspension of sphere with a very low concentration to find the effective viscosity.     

Stages of the cerebral mechanisms of deceptive responses

Cerebral mechanisms of perceiving and telling lies were studied by recording event-related potentials (ERPs) both after an actual deceptive response and during the time interval when the subject decided to tell a lie. Ten healthy volunteers participated in the study. The test consisted of their playing a game against a computer. The subjects could choose between deceptive and truthful answers so as to win the game. The subjects gave a deceptive answer intentionally, the structure of the test ensuring equal numbers of deceptive and truthful answers. The relaxation times in the cases of truthful and deceptive answers did not differ significantly from each other. The comparison of ERPs accompanying deceptive and truthful answers showed the existence of a negativity with a latent period of 90 ms in the regions of the right frontal, central, and right parietal derivations. This negativity indicated that the brain reacted to a deceptive answer even if this a priori “erroneous” act ensured reaching the goal and, in this sense, was subjectively relevant. In terms of the cerebral error detector mechanism, this phenomenon may be regarded as a special case of a general response of the brain to giving an incorrect (deceptive) answer, rather than a response to a lie per se. The interval of time when, presumably, the decision on a deceptive answer was being made was found to contain the late positive component P540, which is most likely to be involved in the preparation of the deceptive answer and the intention to tell a lie.     

Analysis of Protein Structural Motifs in Terms of Sets of Codes Representing Local Structures

An amino acid sequence pattern conserved among a family of proteins is called motif. It is usually related to the specific function of the family. On the other hand, functions of proteins are realized through their 3D structures. Specific local structures, called structural motifs, are considered as related to their functions. However, searching for common structural motifs in different proteins is much more difficult than for common sequence motifs. We are attempting in this study to convert the information about the structural motifs into a set of one-dimensional digital strings, i.e., a set of codes, to compare them more easily by computer and to investigate their relationship to functions more quantitatively. By applying the Delaunay tessellation to a 3D structure of a protein, we can assign each local structure to a unique code that is defined so as to reflect its structural feature. Since a structural motif is defined as a set of the local structures in this paper, the structural motif is represented by a set of the codes. In order to examine the ability of the set of the codes to distinguish differences among the sets of local structures with a given PROSITE pattern that contain both true and false positives, we clustered them by introducing a similarity measure among the set of the codes. The obtained clustering shows a good agreement with other results by direct structural comparison methods such as a superposition method. The structural motifs in homologous proteins are also properly clustered according to their sources. These results suggest that the structural motifs can be well characterized by these sets of the codes, and that the method can be utilized in comparing structural motifs and relating them with function.     

Methods of aggregation of variables in population dynamics

In ecology, we are faced with modelling complex systems involving many variables corresponding to interacting populations structured in different compartmental classes, ages and spatial patches. Models that incorporate such a variety of aspects would lead to systems of equations with many variables and parameters. Mathematical analysis of these models would, in general, be impossible. In many real cases, the dynamics of the system corresponds to two or more time scales. For example, individual decisions can be rapid in comparison to growth of the populations. In that case, it is possible to perform aggregation methods that allow one to build a reduced model that governs the dynamics of a lower dimensional system, at a slow time scale. In this article, we present a review of aggregation methods for time continuous systems as well as for discrete models. We also present applications in population dynamics. A first example concerns a continuous time model of a single population distributed on a system of two connected patches (a logistic source and a sink), by fast migration. It is shown that under a certain condition, the total equilibrium population can be larger than the carrying capacity of the logistic source. A second example concerns a discrete model of a population distributed on two patches, still a source and a sink, connected by fast migration. The use of aggregation methods permits us to conclude that density-dependent migration can stabilize the total population.     

The Significance of Non-vertical Transmission of Phenotype for the Evolution of Altruism

My aim in this paper is to demonstrate that a very simple learning rule based on imitation can help to sustain altruism as a culturally transmitted pattern or behaviour among agents playing a standard prisoner’s dilemma game. The point of this demonstration is not to prove that imitation is single-handedly responsible for existing levels of altruism (a thesis that is false), nor is the point to show that imitation is an important factor in explanations for the evolution of altruism (a thesis already prominent in the existing literature). The point is to show that imitation contributes to the evolution of altruism in a particular way that is not always fairly represented by evolutionary game theory models. Specifically, the paper uses a simple model to illustrate that cultural transmission includes mechanisms that do not transmit phenotype vertically (i.e. from parent to related offspring) and that these mechanisms can promote altruism in the absence of any direct biological propensity favouring such behaviour. This is a noteworthy result because it shows that evolutionary models can be built to explicitly reflect the contribution of non-vertical transmission in our explanations for the evolution of altruism among humans and other social species.     

Possible mechanisms of implementation of toxic potential of lipopolysaccharides of pathogenic bacteria

The significance of variability of biological properties of lipopolysaccharides (LPS) is discussed in the paper within the pathogenesis of infectious process. On the basis of an analysis of published data and of results of independent research of two microorganisms (Yersinia pestis and Francisella tularensis) a conclusion is made on that a biologically inert LPS form (with a weak cytokine-inducing ability, apirogenicity and non-toxicity etc.) is typical of highly pathogenic bacteria. It is suggested that the above phenomenon is biologically expedient. Presumably, the inert LPS transforms to the active form inside a sensitive host and, according to an infection stage, each of them being functionally significant. It is the inert status of LPS that enables the pathogens, at the initial stages, to surmount freely the humoral and cell barriers of host. As the infection progressively aggravates and the proliferation of bacteria modifies itself due to LPS micro- and macroorganisms, its chemical structure and biopolymer conformation change. Both modification mechanisms enhance the LPS toxic potential. In case of a sensitive host, such variations transform the biologically inert LPS into a toxically active form with its function of endotoxin being realized. There is no LPS modification in a host insensitive to such infection, which entails either recovery or prolonged persistence of the pathogen inside the microorganism.     

Certification of Probability of Sterilization of Liquid by Filtration

Four types of hydrosol filters, two reusable (diatomaceous cylinder and fritted-glass funnel) and two disposable (asbestos pad and membrane filter) were challenged with a heavy bacterial suspension to assess their ability to produce sterile filtrates. Two of the four diatomaceous earth filters, the four fritted-glass funnels, and all of the asbestos pads tested generally gave sterile filtrates. However, only one type of filter, one of the membranes in its manufacturer's own holder, consistently gave sterile filtrates. The two other types of membranes usually gave sterile filtrates if tested in one manufacturer's holder, but all types invariably gave contaminated filtrates when tested in another manufacturer's holder. Contaminated filtrates were generally attributed to a poor reusable filter or to a faulty holder used with a disposable filter. If a high degree of certainty is required for sterile heat-labile filtrate, it is suggested that the liquid be passed through two or more filters in a previously tested and proven system.     

Detection of high levels of recombination generated during PCR amplification of RNA templates

Recombination during the PCR amplification of DNA templates can be a serious problem for those seeking to genotype heterogeneous populations, yet a boon to those seeking to enhance variation during in vitro evolution. Here, the extent to which PCR generates chimeric full-length products was estimated using a powerful restriction fragment-length polymorphism (RFLP) assay involving the use of fluorescently labeled PCR primers. Three different RNA-encoding DNA templates were assayed: (i) one for a group I ribozyme, (ii) one for a 16S ribosomal RNA (rRNA), and (iii) one for a messenger RNA (mRNA). In all cases, the observed frequency of chimeric PCR products exceeded 20%, and longer templates appear to produce more chimeric products. Although two of these templates have the potential to form secondary structures during the PCR, this tendency does not seem to heighten recombination frequency. These results corroborate previous studies that show that the production of chimeras can be best attenuated to a certain extent by varying the extension times in PCR.