Proton-dependent electron transfer from CuA to heme a and altered EPR spectra in mutants close to heme a of cytochrome oxidase

Eukaryotic cytochrome c oxidase (CcO) and homologous prokaryotic forms of Rhodobacter and Paraccocus differ in the EPR spectrum of heme a. It was noted that a histidine ligand of heme a (H102) is hydrogen bonded to serine in Rhodobacter (S44) and Paraccocus CcOs, in contrast to glycine in the bovine enzyme. Mutation of S44 to glycine shifts the heme a EPR signal from g(z) = 2.82 to 2.86, closer to bovine heme a at 3.03, without modifying other properties. Mutation to aspartate, however, results in an oppositely shifted and split heme a EPR signal of g(z) = 2.72/2.78, accompanied by lower activity and drastically inhibited intrinsic electron transfer from CuA to heme a. This intrinsic rate is biphasic; the proportion that is slow is pH dependent, as is the relative intensity of the two EPR signal components. At pH 8, the heme a EPR signal at 2.72 is most intense, and the electron transfer rate (CuA to heme a) is 10-130 s(-1), compared to wild-type at 90,000 s(-1). At pH 5.5, the signal at 2.78 is intensified, and a biphasic rate is observed, 50% fast (approximately wild type) and 50% slow (90 s(-1)). The data support the prediction that the hydrogen-bonding partner of the histidine ligand of heme a is one determinant of the EPR spectral difference between bovine and bacterial CcO. We further demonstrate that the heme a redox potential can be dramatically altered by a nearby carboxyl, whose protonation leads to a proton-coupled electron transfer process.     

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.     

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.     

Supergenes in polymorphic land snails. II. Partula suturalis.

The colour and banding of the shell of Partula suturalis are controlled by a single locus (M) with a series of at least six alleles. MX, giving apex as a homozygote, is dominant to MF1, giving frenata, which is dominant to the other alleles. MF2 is similar to MF1 except in its relation with MA. MF2MA produces bisecta and provides a striking example of a heterozygote that is qualitatively different from both homozygotes for the alleles producing it. MA gives atra as a homozygote and is dominant to MC and MS. MC, giving cestata as a homozygote, is recessive to all except MS. MS, giving strigata, is the universal recessive. It is suggested that the locus may be complex. The direction of coiling of the shell is determined by the H locus with HS (sinistrality) dominant to HD (dextrality). The expression of coiling is delayed by one generation, the maternal genotype determining the phenotype of the offspring. M and H are not linked. Self-fertilisation occurs infrequently and non-randomly.     

A nonlinear autoregressive Volterra model of the Hodgkin–Huxley equations

We propose a new variant of Volterra-type model with a nonlinear auto-regressive (NAR) component that is a suitable framework for describing the process of AP generation by the neuron membrane potential, and we apply it to input-output data generated by the Hodgkin–Huxley (H–H) equations. Volterra models use a functional series expansion to describe the input-output relation for most nonlinear dynamic systems, and are applicable to a wide range of physiologic systems. It is difficult, however, to apply the Volterra methodology to the H–H model because is characterized by distinct subthreshold and suprathreshold dynamics. When threshold is crossed, an autonomous action potential (AP) is generated, the output becomes temporarily decoupled from the input, and the standard Volterra model fails. Therefore, in our framework, whenever membrane potential exceeds some threshold, it is taken as a second input to a dual-input Volterra model. This model correctly predicts membrane voltage deflection both within the subthreshold region and during APs. Moreover, the model naturally generates a post-AP afterpotential and refractory period. It is known that the H–H model converges to a limit cycle in response to a constant current injection. This behavior is correctly predicted by the proposed model, while the standard Volterra model is incapable of generating such limit cycle behavior. The inclusion of cross-kernels, which describe the nonlinear interactions between the exogenous and autoregressive inputs, is found to be absolutely necessary. The proposed model is general, non-parametric, and data-derived.     

Logical Probability and Risk Assessment

A risk assessment is intended to provide a statement of current knowledge which is intended to inform a decision-maker of the current state of knowledge in response to a particular concern. Because answering the concerns of decision-makers often requires inferences to be drawn, doubt often arises over how the inference is to be drawn. In quantitative risk assessment, where a mathematical equation or model is used to draw the inference, this uncertainty is referred to as model uncertainty. A two-step process, which is referred to as logical probability, is proposed as a technique for representing model uncertainty in a risk assessment. The first step involves assigning model weights in which the degree of evidential support for each of the alternative models is considered. The second step involves assigning a unique interval in the range of 0 to 1 for each model which reflects the models' weight, to form a probability distribution. While the second step is straightforward, the first step is not. Assigning model weights requires consideration of any line of evidence that may reasonably impact the validity of the assertion of a model. While the development of a procedure for doing so may be expected to be a process which reflects the subjective preferences of whomever is involved in creating it, there are some historical precedents on which to build. Foremost among these are (1) the use of a correlation coefficient or other goodness-of-fit criteria to measure the degree of correspondence between a given model and a set of observations which are used as evidence to support it, and (2) preference given to models which are simpler, which may be ascertained as the number of adjustable parameters the model contains. Additional principles, which have little or no tradition to stand on, must be used to reflect the impact of other empirically supported beliefs on model preference. The procedure proposed is comparable to the procedure known as decision analysis, in which probabilities are assigned to alternative models based on expert or subjective input. The principal difference in the present case is that it is suggested that principles which transcend the decision at hand should be sought and articulated in order to generate a consistent measure of uncertainty arising from interpretation.     

A multiphysics approach for modeling early atherosclerosis

This work is devoted to the development of a mathematical model of the early stages of atherosclerosis incorporating processes of all time scales of the disease and to show their interactions. The cardiovascular mechanics is modeled by a fluid–structure interaction approach coupling a non-Newtonian fluid to a hyperelastic solid undergoing anisotropic growth and a change of its constitutive equation. Additionally, the transport of low-density lipoproteins and its penetration through the endothelium is considered by a coupled set of advection–diffusion-reaction equations. Thereby, the permeability of the endothelium is wall-shear stress modulated resulting in a locally varying accumulation of foam cells triggering a novel growth and remodeling formulation. The model is calibrated and applied to an murine-specific case study, and a qualitative validation of the computational results is performed. The model is utilized to further investigate the influence of the pulsatile blood flow and the compliance of the artery wall to the atherosclerotic process. The computational results imply that the pulsatile blood flow is crucial, whereas the compliance of the aorta has only a minor influence on atherosclerosis. Further, it is shown that the novel model is capable to produce a narrowing of the vessel lumen inducing an adaption of the endothelial permeability pattern.     

Design of a Virtual Player for Joint Improvisation with Humans in the Mirror Game

Joint improvisation is often observed among humans performing joint action tasks. Exploring the underlying cognitive and neural mechanisms behind the emergence of joint improvisation is an open research challenge. This paper investigates jointly improvised movements between two participants in the mirror game, a paradigmatic joint task example. First, experiments involving movement coordination of different dyads of human players are performed in order to build a human benchmark. No designation of leader and follower is given beforehand. We find that joint improvisation is characterized by the lack of a leader and high levels of movement synchronization. Then, a theoretical model is proposed to capture some features of their interaction, and a set of experiments is carried out to test and validate the model ability to reproduce the experimental observations. Furthermore, the model is used to drive a computer avatar able to successfully improvise joint motion with a human participant in real time. Finally, a convergence analysis of the proposed model is carried out to confirm its ability to reproduce joint movements between the participants.     

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.     

Compliance with growth hormone treatment - is it a problem?

Treatments fail for a number of reasons. These include the failure of medicines at a molecular level, failure to achieve the correct diagnosis and therefore use of the correct medication, problems surrounding the doctor-patient relationship, and failure of the service to meet patients' expectations. Compliance is characteristically viewed as the major cause of treatment failures but implicit in the use of the term compliance is the reliance on an imbalance of power where the patient follows what is ordered. Such an approach is likely to lead to failure. A better model is concerned with promoting the full participation of the patient to generate a therapeutic alliance. Despite the need for parental administration and a daily therapeutic regimen there appears to be little evidence to suggest that concordance is a major problem in growth hormone therapy. This is probably because treatment administration relies on the presence of a carer and there are tangible effects. However, concordance is likely to be an issue where there is mismatch between the patient's expectations and those of the doctor. Such a situation may arise when the therapeutic margin is narrow or the therapeutic effect minimal. To resolve this situation, adequate pre-intervention discussion is essential, which should include a clear statement of short- and long-term treatment targets and the likelihood of these being achieved or not. Carefully constructed health care plans are the key and should include educational programmes, home support and regular reinforcement. When concordance problems are suspected, careful consideration needs to be given as to whether the diagnosis is correct, is the treatment really effective and appropriate and does the patient really want the treatment.     

Serial rebinding of ligands to clustered receptors as exemplified by bacterial chemotaxis

Serial ligation is the repeated reversible binding of a ligand to one receptor after another. It is a widespread phenomenon throughout biochemical systems, occurring anytime receptors are clustered together and ligand binding is reversible. Computer simulations are used in this work to investigate a representative example, which is the serial ligation of an extracellular aspartate molecule to the membrane-bound chemotaxis receptors of an Escherichia coli bacterium. It is found that the initial binding site of a ligand to a cluster of receptors is more likely to be near the edge of the cluster than near the middle, although there is no overall bias when all rebindings are considered. Serial ligation does not lead directly to signal amplification or attenuation but instead causes binding events to be correlated in both space and time: a ligand is likely to bind many times in rapid succession in a small region of the receptor cluster, but there can also be long intervals between bindings. This leads to an increased level of noise in the received signal but may allow a single ligand to be sensed above a uniform level of background noise. The focus of this paper is on the interpretation of simulation results so they can be generalized to a wide variety of other systems and to allow the identification of systems in which serial ligation is likely to be important. In the process, several characteristic times are identified, as are scaling laws for the spatial and temporal dynamics.     

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.     

A centrosomal theory of the short term evolutionary maintenance of sexual reproduction

A new mode of inheritance is postulated in which a sexual offspring receives a contribution from each parent and selects the better to pass on to its own offspring. This could provide a simple advantage to sex over a sex whose magnitude is shown to be of the order of a doubling of fitness in each generation, large enough to cancel the twofold cost of sex. This possible advantage to sex can be realized only if a cell component is in fact inherited in this selectively ambiguous way. No such component is known of, but the eukaryotic centrosome is a possible candidate. The possibility is discussed that the centrosome contains an obligatorily non-digital replicator which has an essential function in the initiation of microtubules. If this theory is true, it has the capacity to apply as widely as sex is found, and it would rescue theories of the long-term maintenance of sex from the necessity to provide a twofold advantage in each generation. If false, the theory will soon be disproved.     

The effect of gene flow on the coalescent time in the human-chimpanzee ancestral population

The coalescent process in the human-chimpanzee ancestral population is investigated using a model, which incorporates a certain time period of gene flow during the speciation process. a is a parameter to represent the degree and time of gene flow, and the model is identical to the null model with an instantaneous species split when a=infinity. A maximum likelihood (ML) method is developed to estimate a, and its power and reliability is investigated by coalescent simulations. The ML method is applied to nucleotide divergence data between human and chimpanzee. It is found that the null model with an instantaneous species split explains the data best, and no strong evidence for gene flow is detected. The result is discussed in the view of the mode of speciation. Another ML method is developed to estimate the male-female ratio (alpha) of mutation rate, in which the coalescent process in the ancestral population is taken into account.     

Micropipette Aspiration of Substrate-attached Cells to Estimate Cell Stiffness

Growing number of studies show that biomechanical properties of individual cells play major roles in multiple cellular functions, including cell proliferation, differentiation, migration and cell-cell interactions. The two key parameters of cellular biomechanics are cellular deformability or stiffness and the ability of the cells to contract and generate force. Here we describe a quick and simple method to estimate cell stiffness by measuring the degree of membrane deformation in response to negative pressure applied by a glass micropipette to the cell surface, a technique that is called Micropipette Aspiration or Microaspiration.Microaspiration is performed by pulling a glass capillary to create a micropipette with a very small tip (2-50 μm diameter depending on the size of a cell or a tissue sample), which is then connected to a pneumatic pressure transducer and brought to a close vicinity of a cell under a microscope. When the tip of the pipette touches a cell, a step of negative pressure is applied to the pipette by the pneumatic pressure transducer generating well-defined pressure on the cell membrane. In response to pressure, the membrane is aspirated into the pipette and progressive membrane deformation or "membrane projection" into the pipette is measured as a function of time. The basic principle of this experimental approach is that the degree of membrane deformation in response to a defined mechanical force is a function of membrane stiffness. The stiffer the membrane is, the slower the rate of membrane deformation and the shorter the steady-state aspiration length.The technique can be performed on isolated cells, both in suspension and substrate-attached, large organelles, and liposomes.Analysis is performed by comparing maximal membrane deformations achieved under a given pressure for different cell populations or experimental conditions. A "stiffness coefficient" is estimated by plotting the aspirated length of membrane deformation as a function of the applied pressure. Furthermore, the data can be further analyzed to estimate the Young''s modulus of the cells (E), the most common parameter to characterize stiffness of materials. It is important to note that plasma membranes of eukaryotic cells can be viewed as a bi-component system where membrane lipid bilayer is underlied by the sub-membrane cytoskeleton and that it is the cytoskeleton that constitutes the mechanical scaffold of the membrane and dominates the deformability of the cellular envelope. This approach, therefore, allows probing the biomechanical properties of the sub-membrane cytoskeleton.     

Simple sequential boundaries for treatment selection in multi-armed randomized clinical trials with a control

Summary .   In situations when many regimens are possible candidates for a large phase III study, but too few resources are available to evaluate each relative to the standard, conducting a multi-armed randomized selection trial is a useful strategy to remove inferior treatments from further consideration. When the study has a relatively quick endpoint such as an imaging-based lesion volume change in acute stroke patients, frequent interim monitoring of the trial is ethically and practically appealing to clinicians. In this article, I propose a class of sequential selection boundaries for multi-armed clinical trials, in which the objective is to select a treatment with a clinically significant improvement upon the control group, or to declare futility if no such treatment exists. The proposed boundaries are easy to implement in a blinded fashion, and can be applied on a flexible monitoring schedule in terms of calendar time. Design calibration with respect to prespecified levels of confidence is simple, and can be accomplished when the response rate of the control group is known only up to an interval. One of the proposed methods is applied to redesign a selection trial with an imaging endpoint in acute stroke patients, and is compared to an optimal two-stage design via simulations: The proposed method imposes smaller sample size on average than the two-stage design; this advantage is substantial when there is in fact a superior treatment to the control group.     

Extending the viability theory framework of resilience to uncertain dynamics,and application to lake eutrophication

Resilience, the capacity for a system to recover from a perturbation so as to keep its properties and functions, is of growing concern to a wide range of environmental systems. The challenge is often to render this concept operational without betraying it, nor diluting its content. The focus here is on building on the viability theory framework of resilience to extend it to discrete-time stochastic dynamical systems. The viability framework describes properties of the system as a subset of its state space. This property is resilient to a perturbation if it can be recovered and kept by the system after a perturbation: its trajectory can come back and stay in the subset. This is shown to reflect a general definition of resilience. With stochastic dynamics, the stochastic viability kernel describes the robust states, in which the system has a high probability of staying in the subset for a long time. Then, probability of resilience is defined as the maximal probability that the system reaches a robust state within a time horizon. Management strategies that maximize the probability of resilience can be found through dynamic programming. It is then possible to compute a range of statistics on the time for restoring the property. The approach is illustrated on the example of lake eutrophication and shown to foster the use of different indicators that are adapted to distinct situations. Its relevance for the management of ecological systems is also discussed.     

Haplotyping for disease association: a combinatorial approach

We consider a combinatorial problem derived from haplotyping a population with respect to a genetic disease, either recessive or dominant. Given a set of individuals, partitioned into healthy and diseased, and the corresponding sets of genotypes, we want to infer "bad' and "good' haplotypes to account for these genotypes and for the disease. Assume e.g. the disease is recessive. Then, the resolving haplotypes must consist of bad and good haplotypes, so that (i) each genotype belonging to a diseased individual is explained by a pair of bad haplotypes and (ii) each genotype belonging to a healthy individual is explained by a pair of haplotypes of which at least one is good. We prove that the associated decision problem is NP-complete. However, we also prove that there is a simple solution, provided the data satisfy a very weak requirement.     

Signalling: basics and evolution

Signalling concerns the transfer of information from one body, a source, to another, a receiver in order to stimulate activity. The problem arises with the word information. It is defined as what is transferred in a sequence of things, say between people, e.g. words or signs. The idea of signalling between people is then obvious but it is not clear in cell biology. Information transfer, signalling, is required for the organisation of all cellular activity but we must ask what is transferred and how is it transmitted and received? Sometimes it is assumed that all information, i.e. organisation in a cell, is represented in the DNA sequence. This is incorrect. We shall show that the environment is a second source of information concerning material and energy. The receiving party from both DNA and the environment is general metabolism. The metabolism then signals back and sends information to both DNA and uptake from the environment. Even then energy is needed with machinery to send out all signals. This paper examines the way signalling evolved from prokaryotes through to man. In this process the environmental information received increased to the extent that finally the brain is a phenotypic as much as a genotypic organ within a whole organism. By phenotypic we mean it is organised by and interactive with information from the environment.     

PLANNING THE RATIONAL USE OF WETLANDS

SUMMARY

A conceptual approach to planning is outlined. It is a cyclical process in which we start with a goal, examine it and express it more clearly, assemble information, evaluate the information, work out alternative lines of action, choose the one most likely to lead to success and then try it out.

This approach is applied to wetlands. The importance of establishing a “unity of action” and a body to co-ordinate activities is stressed. Planning the conservation of estuaries in Natal is given as a practical example.

A number of research projects is given in relation to the planning process. A comprehensive and methodical means of determining research projects is advocated.

The paper concludes with a call for committment, else planning is an exercise in futility.