Effect of binding on melting transitions in polymer–diluent systems

An expression is derived for the melting point of a polymer when in equilibrium with a solution in which binding of low molecular weight compounds to the polymer takes place. Allowance is made for the possibility that the crystalline polymer itself is a complex. The argument is a purely thermodynamic one and is based on a consideration of the change in free energy as a result of a change in binding. Allowance is made also for non-specific polymer–solvent interactions, in which the mixture of low molecular weight solvents is treated as a single solvent. Special attention is paid to “inverted” melting transitions, i.e., cases in which the melting point increases with increasing dilution of the polymer. It is shown that as a rule this is accompanied by a corresponding, inverted effect of the solvent composition on the melting point. It is further shown that-in the absence of binding, “normal” behavior at the critical point (i.e., phase separation is induced by lowering the temperature) is always accompanied by “normal” melting behavior (i.e., a decrease in melting point when the polymer is diluted). Also, “inverted” melting always implies that phase separation at the critical point is induced by heating, but the reverse is not necessarily true.     

The modelling of fibre reorientation in soft tissue

In this paper, a hyperelastic and thermodynamically consistent model for soft tissue is developed that is able to describe the change of the initial orientation of the collagen fibres. Full numerical implementation is considered as well. The collagen architecture is assumed to reorient driven by a specific thermodynamical force. The anisotropy is described by a strain energy function, which is decomposed into a part related to the matrix and a part related to the fibres. The initial fibre orientation is defined by a structural tensor, while the current orientation is described by a time-dependent structural tensor, which results from the initial one by a rotational transformation. The rotation tensor is obtained via an integration process of a rate tensor, which depends on an adequately defined thermodynamical force. The integration is achieved via an exponential map algorithm, where it is shown that the rotation is necessarily a two-parametric one. Efficiency of the proposed formulation is demonstrated using some numerical examples.     

A graph theoretic approach to the development of minimal phylogenetic trees

Summary The problem of determining the minimal phylogenetic tree is discussed in relation to graph theory. It is shown that this problem is an example of the Steiner problem in graphs which is to connect a set of points by a minimal length network where new points can be added. There is no reported method of solving realistically-sized Steiner problems in reasonable computing time. A heuristic method of approaching the phylogenetic problem is presented, together with a worked example with 7 mammalian cytochrome c sequences. It is shown in this case that the method develops a phylogenetic tree that has the smallest possible number of amino acid replacements. The potential and limitations of the method are discussed. It is stressed that objective methods must be used for comparing different trees. In particular it should be determined how close a given tree is to a mathematically determined lower bound. A theorem is proved which is used to establish a lower bound on the length of any tree and if a tree is found with a length equal to the lower bound, then no shorter tree can exist.     

Rhesus monkey apolipoprotein(a). Sequence, evolution, and sites of synthesis

Human lipoprotein(a) is a low density lipoprotein-like lipoprotein whose concentration in plasma is correlated with atherosclerosis. The characteristic protein component of lipoprotein(a) is apolipoprotein(a) (apo(a)) which is disulfide-linked to apolipoprotein B-100. Sequencing of rhesus monkey apo(a) cDNA suggests that this protein, like human apo(a), is highly similar to plasminogen. Sequence data suggests that a plasminogen-like protease activity and kringle 1-, 2-, 3-, and 5-like domains are unnecessary for apo(a) function, but a highly repeated kringle four-like domain is important. Liver is the major site of apo(a) RNA synthesis; reduced amounts of message were also found in testes and brain. Co-expression with apoB-100 and plasminogen in rhesus tissues is not mandatory.     

A physical characterization of biological information and communication system model of ecosystems

What is information for living organisms? An answer to this question is given on a physical basis and a contrast between genetic information and sensory information is stressed with a relation to information theory. A simple model of an environment of living organisms is investigated on the basis of communication systems model proposed by the author and a cost of information transmission is taken into consideration through capacity cost theory. It is shown that channel capacity of information theory can be interpreted as an environment, and furthermore that a large diversity of genetic messages needs a large capacity of the environment. In addition, a definition of life in terms of information is proposed and a unified view on life processes is suggested.     

On religious ritual as deference and communicative excess

I shall argue that most religious ritual is a performance that not only invokes but also performs communication. The ethnographic material from which I derive this argument is from China, in particular the temple rituals of local festivals. My argument is that a deep obeisance of welcome and departure that is both like and not like the normal ritual of greeting marks a religious from a non-religious ritual occasion and place. It is a ritual doubling that makes the honoured guest also a host. Religious ritual is a medium, and as a medium it is double in another sense. It is deference and deferral, a repeated transmission of obeisance to authority that has the authority of repetition. As well as doubling, religious ritual is excessively communicative. The medium is a performance not only of invitation and departure but also of communicative response, and it repeats this communication as a test of communicative response over and over again. Religious ritual performs both the opening and closing of communication, both the seeking and the responsive reciprocation of gift offerings with bounteousness. It is shadowed by the possibility of no response, of giving offence, of being abandoned. This possibility is acknowledged by being prevented, while the possibility that the performers are their own responders is disavowed.     

Fluorescence polarization immunoassay: detection of antibody to Brucella abortus

Fluorescence polarization immunoassay (FPA) is a homogeneous immunoassay useful for rapid and accurate detection of antibody or antigen. The principle of the assay is that a fluorescent dye (attached to an antigen or an antibody fragment) can be excited by plane-polarized light at the appropriate wavelength. As a rule, a small molecule rotates faster when in solution than a larger molecule. The rotation rate may be assessed by measuring light intensity in the vertical and horizontal planes. Generally, the time it takes a molecule to rotate through a given angle is an indication of its size. When a small molecule that rotates rapidly is bound to a larger molecule, the rotation rate is decreased and this decrease is measured. Because it is a primary antigen-antibody interaction, the rate of reaction is very rapid and usually a result may be obtained in minutes. This technology was applied to the detection of antibody to Brucella abortus in serum and milk, providing for the first time a rapid primary binding assay that is cost effective for use in the field.     

Forming sparse representations by local anti-Hebbian learning

How does the brain form a useful representation of its environment? It is shown here that a layer of simple Hebbian units connected by modifiable anti-Hebbian feed-back connections can learn to code a set of patterns in such a way that statistical dependency between the elements of the representation is reduced, while information is preserved. The resulting code is sparse, which is favourable if it is to be used as input to a subsequent supervised associative layer. The operation of the network is demonstrated on two simple problems.     

Toward an optimal design principle in relational biology

A vulnerability criterion is posed for a biological system within the context of representing the system as a relational set, i.e., a collection of components whose interdependency is described by means of a set of binary relations. The criterion provides a numerical value for each representation and therefore a means for comparing one representation against another. Choice of the criterion is such that the larger a numerical value a representation has then the less vulnerable to destruction is the system represented. Other things being equal, it is argued that the representation which endows the system with the least vulnerability is more likely to be a valid representation. A selection criterion is thereby achieved for narrowing down the choice ofa priori representations.     

Length control of extended protein structures in bacteria and bacteriophages

The length of the tail of bacteriophages is controlled by a protein which acts as a molecular ruler. The needle of the injectisome, which is assembled by the polymerization of subunits that are exported through the nascent injectisome, is functionally related to the tail of bacteriophages. Interestingly, its length is controlled by a protein, which is itself exported and acts as a molecular ruler that is coupled to a substrate specificity switch. The bacterial flagellum is evolutionarily related to the injectisome. The length of the hook is also controlled by a secreted protein. This protein acts as a substrate specificity switch and, possibly, also as a ruler.     

Evidence for a presynaptic blockage of transmission in a temperature-sensitive mutant of Drosophila

In the temperature sensitive mutant of Drosophila, shibirets1 (shi), synaptic transmission in the dorsal longitudinal flight muscles (DLM) is normal at 19 degrees C, but is diminished progressively as the temperature is raised, and is blocked at 29 degrees C. The purpose of this paper is to determine whether this defect is located presynaptically, postsynaptically, or both. It is demonstrated here that the postsynaptic sensitivity to L-glutamate, the putative transmitter for this synapse, is not decreased at 29 degrees C. Furthermore, studies conducted with genetic mosaics of this mutant show that transmission is blocked when a mutant motor neuron synapses on a wild-type muscle fiber, but is not blocked when a wild-type motor neuron synapses on a mutant muscle fiber. Thus, the shi phenotype (temperature dependent transmission block) correlates with a shi motor neuron, not with a shi muscle fiber. The data, therefore, suggest that the defect is not postsynaptic, but presynaptic.     

A self-organized chemical model and reaction cascade

Some reaction cascades in biological systems are analyzed by a self-organized chemical model, an autocatalytic reaction. This model is described by the coupling of a primary system which stabilizes the initial stage of the reaction rapidly and a partial system which controls the primary system slowly. By the internal force caused by a trigger above the threshold, the coupled system in near-equilibrium is broken and changed into a new state. From the rate equation for the coupled system, a dimensionless nonlinear state equation, n = -n3 - un - v, is derived, where n is the concentration of intermediate, and u, v are dynamic variables of the system. This equation is similar to a nonequilibrium tri-molecular reaction. By using this chemical network theory, fibrin polymerization. F + F----fm----fp + X, where F is a fibrinogen molecule, fm is a fibrin monomer, fp is fibrin polymer, and X is small peptides released from fibrinogen, is discussed as an excellent example of the enzyme reaction cascade.     

Formation of segregated regions of feature detecting cells in self-organizing nerve field

This paper investigates the formation of a segregated region for a specific set of input signals in a nerve field. The segregated region is formed by a feature detecting cell group which fires only for a specific set of input signals. This firing region is called the region of feature detecting cells for the corresponding input set. First, a basic self-organizing model is given. The model is composed of the first input layer, the second nerve cell layer with lateral inhibitory interactions (it is called a lateral-inhibition type nerve field) and an inhibitory nerve cell. An input signal is an-dimensional vector whose components assume continuous values. Next, the condition which gurantees the formation of a segregated region for a specific set of input signals is derived, and the properties of the model are discussed based on the derived condition. In addition, the behavior of the model is examined through computer-simulated experiments. The following observations are made: When a certain condition is satisfied, a segregated region is formed in the nerve field according to a specific set of input signals. By varying the parameters of learning, the region is formed depending on the similarity between input signals. The regions for similar input signals are formed near each other in the nerve field. The region is created depending on the occurence probability of the input signal and its norm.     

Ewens' sampling formula and related formulae: combinatorial proofs, extensions to variable population size and applications to ages of alleles

Ewens' sampling formula, the probability distribution of a configuration of alleles in a sample of genes under the infinitely-many-alleles model of mutation, is proved by a direct combinatorial argument. The distribution is extended to a model where the population size may vary back in time. The distribution of age-ordered frequencies in the population is also derived in the model, extending the GEM distribution of age-ordered frequencies in a model with a constant-sized population. The genealogy of a rare allele is studied using a combinatorial approach. A connection is explored between the distribution of age-ordered frequencies and ladder indices and heights in a sequence of random variables. In a sample of n genes the connection is with ladder heights and indices in a sequence of draws from an urn containing balls labelled 1,2,...,n; and in the population the connection is with ladder heights and indices in a sequence of independent uniform random variables.     

A nonlinear integral equation for visual impedance

The Hartline-Ratliff equation is a linear integral equation of the second kind and is employed in modeling inhibitory networks. Saturation of the inhibiting elements is commonly modeled as a function whose form is sigmoid; however, the resulting integral equation is nonlinear. Whenever the unknown function within the integral is hypothesized to be a nondecreasing nonlinear function, the Hartline-Ratliff equation becomes a nonlinear integral equation of the Hammerstein type. We present existence and uniqueness theorems for a Hammerstein equation which represents a further generalization of the Hartline-Ratliff equation.     

The Influence of Temperature on the Effect of Bacteriostatic Concentrations of Phenol Against Escherichia coli

S ummary . During early exponential growth of Escherichia coli in the absence of phenol there is a natural death rate at 20, 30, and 44° but at the optimum temperature around 37° there is little if any significant death. The influence of a rise in temperature from 20 to 44° is to decrease the generation time and at 44° the lower generation time compensates for a reduced generation index. The main effect of sub-bacteriostatic concentrations of phenol is to increase the generation time but at 30, 37 and 44° there is a significant reduction in the generation index at the higher concentrations resulting in a dynamic bacteriostasis. At 20° bacteriostasis is due mainly to a large generation time but there is a little growth and so bacteriostasis is essentially dynamic. There is also evidence to suggest that the effect of a particular concentration of phenol on the generation index is not merely influenced by the temperature but by the generation time under the particular set of conditions. If phenol is added to rapidly growing cultures of E. coli the effect of a rise in temperature is to reduce the concentration required for bacteriostasis but if it is added during the lag phase there is a maximum in the bacteriostatic concentration between 20 and 37°.     

Universal common ancestry,LUCA, and the Tree of Life: three distinct hypotheses about the evolution of life

Common ancestry is a central feature of the theory of evolution, yet it is not clear what “common ancestry” actually means; nor is it clear how it is related to other terms such as “the Tree of Life” and “the last universal common ancestor”. I argue these terms describe three distinct hypotheses ordered in a logical way: that there is a Tree of Life is a claim about the pattern of evolutionary history, that there is a last universal common ancestor is an ontological claim about the existence of an entity of a specific kind, and that there is universal common ancestry is a claim about a causal pattern in the history of life. With these generalizations in mind, I argue that the existence of a Tree of Life entails a last universal common ancestor, which would entail universal common ancestry, but neither of the converse entailments hold. This allows us to make sense of the debates surrounding the Tree, as well as our lack of knowledge about the last universal common ancestor, while still maintaining the uncontroversial truth of universal common ancestry.     

Competition in chemostat-type equations with two habitats

Competition on a model with nutrient recycling is considered. The model is based on a chemostat-type equation which is used to study population dynamics of microorganisms. The model consists of four organisms competing for a limiting nutrient. Nutrient is supplied both from the in-flow of medium and a recycling with delay, the latter is generated from dead organisms by bacterial decomposition. This paper shows that the model undergoes a Hopf bifurcation through a critical value of time delay when the in-flow is small. Coexistence of four organisms competing for one limiting nutrient is indicated by numerical simulation results.     

The question of virginity testing in Turkey

Pre-marital sex for a woman is regarded as wrong in my country. As a result, it is socially forbidden for a woman to engage in this act. In order to present a woman as a virgin on her marriage day, she is subjected to pressure, and put under control both by her family and societal norms. However, a man is free and never made to suffer any of the above. A woman found to be a virgin on her first night of marriage is seen as a normal person while one suspected to have lost her virginity is made to undergo a series of medical examinations to bring clarity to her situation.