The unfolding of the P pili quaternary structure by stretching is reversible, not plastic

P pili are protein filaments expressed by uropathogenic Escherichia coli that mediate binding to glycolipids on epithelial cell surfaces, which is a prerequisite for bacterial infection. When a bacterium, attached to a cell surface, is exposed to external forces, the pili, which are composed of approximately 10(3) PapA protein subunits arranged in a helical conformation, can elongate by unfolding to a linear conformation. This property is considered important for the ability of a bacterium to withstand shear forces caused by urine flow. It has hitherto been assumed that this elongation is plastic, thus constituting a permanent conformational deformation. We demonstrate, using optical tweezers, that this is not the case; the unfolding of the helical structure to a linear conformation is fully reversible. It is surmised that this reversibility helps the bacteria regain close contact to the host cells after exposure to significant shear forces, which is believed to facilitate their colonization.     

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.     

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.     

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.     

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.     

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.     

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.     

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.     

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.     

A conserved region within the Bordetella pertussis autotransporter BrkA is necessary for folding of its passenger domain

Autotransporter secretion represents a unique mechanism that Gram-negative bacteria employ to deliver proteins to their cell surface. BrkA is a Bordetella pertussis autotransporter protein that mediates serum resistance and contributes to adherence of the bacterium to host cells. BrkA is a 103 kDa protein that is cleaved to form a 73 kDa alpha-domain and a 30 kDa beta domain. The alpha domain, also referred to as the passenger domain, is responsible for the effector functions of the protein, whereas the beta domain serves as a transporter. In an effort to characterize BrkA secretion, we have shown that BrkA has a 42 amino acid signal peptide for transit across the cytoplasmic membrane, and a translocation unit made up of a short linker region fused to the beta-domain to ferry the passenger domain to the bacterial surface through a channel formed by the beta-domain. In this report, we provide genetic, biochemical and structural evidence demonstrating that a region within the BrkA passenger (Glu601-Ala692) is necessary for folding the passenger. This region is not required for surface display in the outer membrane protease OmpT-deficient Escherichia coli strain UT5600. However, a BrkA mutant protein bearing a deletion in this region is susceptible to digestion when expressed in E. coli strains expressing OmpT suggesting that the region is required to maintain a stable structure. The instability of the deletion mutant can be rescued by surface expressing Glu601-Ala692in trans suggesting that this region is acting as an intramolecular chaperone to effect folding of the passenger concurrent with or following translocation across the outer membrane.     

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.     

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.     

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 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.     

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.     

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.     

Fuzzy molecular surfaces.

Surface area of a macromolecule, accessible to a solvent, is defined and calculated, taking into account the probabilistic character of atomic positions due to the high frequency atomic vibrations. For a given a space point, we consider a probability of the event, that this point is covered by a macromolecule. A volume is defined as a space integral of this probability field. The envelope, accessible to a solvent molecule center, becomes fuzzy, existing only in a probabilistic sense. The accessible area is defined as a derivative of the envelope volume with respect to the probe size.     

Image segmentation using a neural network

An object extraction problem based on the Gibbs Random Field model is discussed. The Maximum a'posteriori probability (MAP) estimate of a scene based on a noise-corrupted realization is found to be computationally exponential in nature. A neural network, which is a modified version of that of Hopfield, is suggested for solving the problem. A single neuron is assigned to every pixel. Each neuron is supposed to be connected only to all of its nearest neighbours. The energy function of the network is designed in such a way that its minimum value corresponds to the MAP estimate of the scene. The dynamics of the network are described. A possible hardware realization of a neuron is also suggested. The technique is implemented on a set of noisy images and found to be highly robust and immune to noise.     

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.     

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.