Consideration of the Possibility that the slow step in protein denaturation reactions is due to cis-trans isomerism of proline residues.

A model is proposed to account for the observation that the denaturation of small proteins apparently occurs in two kinetic phases. It is suggested that only one of these phases--the fast one--is actually an unfolding process. The slow phase is assumed to arise from the cis-trans isomerism of proline residues in the denaturated protein. From model compound data, it is shown that the expected rate for isomerism is in satisfactory agreement with the rates actually observed for protein folding. It is also shown that a simple model of protein unfolding based on the isomerism concept is very successful in accounting for many known experimental characteristics of the kinetics and thermodynamic of protein denaturation. Thus, the model is able to predict that two kinetic phases will be seen in the transition region while none are seen in the base-line regions, that both the fast and slow refolding phases lead to the native protein as the product, that the fast phase becomes the only observable phase for jumps ending far in the denatured base-line region, that most or all small proteins show a limiting low-temperature activation energy of ca. 20,000 cal, and that the relaxtion time for the slow phase seen in cytochrome c denaturation is much shorter than for all other small proteins. By utilizing "double-jump" experiments, it is shown directly that the slow phase is not part of the unfolding process but that it corresponds to a transition among two or more denatured forms which have identical spectroscopic (286.5 nm) properties. Thus, the slow relaxation is "invisible" except in the transition region where it couples to the fast unfolding equilibrium. Finally, since the present model assumes that only one of the major kinetic phases seen in denaturation reactions is concerned with the denaturation process per se, it is in agreement with numerous thermodynamic studies which show consistency with the two-state model for unfolding.     

Site of graviperception in roots: a re-examination

Two lines of evidence have been cited to support the assertion that the root cap is the sole site of graviperception in the root. The first evidence is based on surgical removal of the cap, which abolishes the response to gravity. This is sufficient to conclude that the cap is involved in gravitropism, but not to conclude that the cap is the site of graviperception. The second is based on the results of centrifugation experiments, in which different parts of the plant are subjected to different centrifugal forces. The data from such experiments have been cited to support the conclusion that the perception of gravity is limited to the rootcap. However, these data actually support the conclusion that gravity is perceived throughout the root tip, and not only in the root cap. We believe that the data support the conclusion that the root cap is involved in root gravitropism, but that there is inadequate evidence to conclude that the cap is the sole site of graviperception.     

GTPase-dependent signaling in bacteria: characterization of a membrane-binding site for era in Escherichia coli.

Era is an Escherichia coli GTPase that is essential for cell viability and is peripherally associated with the cytoplasmic membrane. Both immunoelectron microscopy and subcellular-fractionation experiments have shown that Era is present in cytoplasmic as well as membrane-associated pools. These data led to speculation that the mechanism of action of Era may require cycling between membrane and cytoplasmic sites. In order to investigate this possibility, an in vitro binding assay was developed to characterize the binding of Era to membrane fractions. Competition and saturation binding experiments suggest that a site that is specific for Era and capable of binding up to 5 ng of Era per microgram of membrane protein is present in membrane preparations. The binding curve is complex, indicating that multiple equilibria describe the interaction. The binding of Era to this putative receptor is dependent on guanine nucleotides; binding cannot be measured in the absence of nucleotide, and neither ATP nor UTP can substitute. Subfractionation of cell walls showed that the guanine nucleotide-dependent binding site was present in fractions enriched in cytoplasmic membrane. These data provide evidence that Era may be involved in a GTPase-receptor-coupled membrane-signaling pathway that is essential for growth in E. coli.     

Neurophysiological mechanisms underlying face processing within and beyond the temporal cortical visual areas.

The ways in which information about faces is represented and stored in the temporal lobe visual areas of primates, as shown by recordings from single neurons in macaques, are considered. Some neurons that respond primarily to faces are found in the cortex in the anterior part of the superior temporal sulcus (in which neurons are especially likely to be tuned to facial expression and to face movement involved in gesture), and in the TE areas more ventrally forming the inferior temporal gyrus (in which neurons are more likely to have responses related to the identity of faces). Quantitative studies of the responses of the neurons that respond differently to the faces of different individuals show that information about the identity of the individual is represented by the responses of a population of neurons, that is, ensemble encoding rather than 'grandmother cell' encoding is used. It is argued that this type of tuning is a delicate compromise between very fine tuning, which has the advantage of low interference in neuronal network operations but the disadvantage of losing the useful properties (such as generalization, completion and graceful degradation) of storage in neuronal networks, and broad tuning, which has the advantage of allowing these properties of neuronal networks to be realized but the disadvantage of leading to interference between the different memories stored in an associative network. There is evidence that the responses of some of these neurons are altered by experience so that new stimuli become incorporated in the network. It is shown that the representation that is built in temporal cortical areas shows considerable invariance for size, contrast, spatial frequency and translation. Thus the representation is in a form which is particularly useful for storage and as an output from the visual system. It is also shown that one of the representations that is built is object based, which is suitable for recognition and as an input to associative memory, and that another is viewer centred, which is appropriate for conveying information about gesture. Ways are considered in which such cortical representations might be built by competitive self-organization aided by back projections in the multi-stage cortical processing hierarchy which has convergence from stage to stage.     

Synonymous Substitution Rates in Enterobacteria

It has been shown previously that the synonymous substitution rate between Escherichia coli and Salmonella typhimurium is lower in highly than in weakly expressed genes, and it has been suggested that this is due to stronger selection for translational efficiency in highly expressed genes as reflected in their greater codon usage bias. This hypothesis is tested here by comparing the substitution rate in codon families with different patterns of synonymous codon use. It is shown that the decline in the substitution rate across expression levels is as great for codon families that do not appear to be subject to selection for translational efficiency as for those that are. This implies that selection on translational efficiency is not responsible for the decline in the substitution rate across genes. It is argued that the most likely explanation for this decline is a decrease in the mutation rate. It is also shown that a simple evolutionary model in which synonymous codon use is determined by a balance between mutation, selection for an optimal codon, and genetic drift predicts that selection should have little effect on the substitution rate in the present case.     

Metabolic stabilization of MAP kinase phosphatase-2 in senescence of human fibroblasts

Cellular senescence is characterized by impaired cell proliferation. We have previously shown that, relative to the young counterpart, senescent WI-38 human fibroblasts display a decreased abundance of active phosphorylated ERK (p-ERK) in the nucleus. We have tested the hypothesis that this is due to elevated levels of nuclear MAP kinase phosphatase (MKP) activity in senescent cells. Our results indicate that the activity and abundance of MKP-2 is increased in senescent fibroblasts, compared to their young counterparts. Further analysis indicates that it is MKP-2 protein, but not MKP-2 mRNA level, that is increased in senescent cells. This increase is the result of the increased stability of MKP-2 protein against proteolytic degradation. The degradation of MKPs was impaired by proteasome inhibitors both in young and old WI-38 cells, indicating that proteasome activity is involved in the degradation of MKPs. Finally, our results indicate that proteasome activity, in general, is diminished in senescent fibroblasts. Taken together, these data indicate that the increased level and activity of MKP-2 in senescent WI-38 cells are the consequence of impaired proteosomal degradation, and this increase is likely to play a significant role in the decreased levels of p-ERK in the nucleus of senescent cells.     

Adaptation of prey and predators between patches

Mathematical models are proposed to simulate migrations of prey and predators between patches. In the absence of predators, it is shown that the adaptation of prey leads to an ideal spatial distribution in the sense that the maximal capacity of each patch is achieved. With the introduction of co-adaptation of predators, it is proved that both prey and predators achieve ideal spatial distributions when the adaptations are weak. Further, it is shown that the adaptation of prey and predators increases the survival probability of predators from the extinction in both patches to the persistence in one patch. It is also demonstrated that there exists a pattern that prey and predators cooperate well through adaptations such that predators are permanent in every patch in the case that predators become extinct in each patch in the absence of adaptations. For strong adaptations, it is proved that the model admits periodic cycles and multiple stability transitions.     

A Structure-Activity Relationship for the Hydrolysis of Acetylamino Acids by Porcine Aminoacylase

A structure-activity relationship is presented that satisfactorily predicts the rates of hydrolysis of a series of acetylglycine derivatives by porcine aminoacylase. It is apparent that the substrate specificity of aminoacylase is mainly kinetic in origin, the observed correlation with Taft's E(s) parameter supporting the notion that enzymolysis proceeds through a mechanism that is analogous to chemical hydrolysis. It is suggested that the alpha-CH(2)CH group of those substrates that possess this moiety is conformationally immobile upon binding. This lock facilitates rapid hydrolysis and results from steric interactions between the enzyme and substrate. The incorporation of alpha-methyl amino acid derivatives in the structure-activity relationship is consistent with a flexible active site model and it is concluded that the alpha-methyl effect in this system is a binding phenomenon. It is evident that the active center of porcine aminoacylase can comfortably accommodate amino acid derivatives with side chains containing less than six carbon atoms, contrary to previous assertions. It is suggested that the binding of bulkier derivatives necessitates the distortion of the active site. Derivatives possessing beta-hydroxyl groups are found to deviate from expected behavior and a nonproductive binding model is presented. Copyright 2000 Academic Press.     

Towards a molecular explanation of the high performance of the tuna heart

The tuna heart is capable of sustaining cardiac outputs that are high relative to other active teleost species. The question as to whether there are known molecular mechanisms to explain this phenomenon is examined. Unfortunately, the evidence at present is scant but the paper attempts to put existing knowledge into a contextual framework. It is known that the high cardiac outputs in tuna are due to the maximum heart rates that are high relative to other active teleost species. While the normalized stroke volume (ml/kg body weight) in tuna is in the same range as that of trout several important points are worth noting. The stroke volume in the tuna heart is generated in the face of an afterload that is two-fold higher (due to high ventral aortic pressure) than that observed in the trout or other teleosts. Since the stroke volume is predicated on the strength of ventricular contraction, the question then arises as to whether this is a consequence of factors intrinsic or extrinsic to the design of the cardiomyocytes that make up the myocardium. Two important extrinsic factors must be noted: the substantially higher normal operating temperatures and the apparent cardiac hyperplasia in the tuna. While the merit of these factors is discussed, the paper focuses on intrinsic factors. There is very little that has been determined to date that would indicate substantive changes in the design of the myocyte in the tuna heart compared to that of trout. Are these extrinsic factors alone then sufficient to account for the impressive cardiac output capabilities in the tuna?     

The forms of knowledge mobilized in some machine vision systems.

This paper describes a number of computer vision systems that we have constructed, and which are firmly based on knowledge of diverse sorts. However, that knowledge is often represented in a way that is only accessible to a limited set of processes, that make limited use of it, and though the knowledge is amenable to change, in practice it can only be changed in rather simple ways. The rest of the paper addresses the questions: (i) what knowledge is mobilized in the furtherance of a perceptual task?; (ii) how is that knowledge represented?; and (iii) how is that knowledge mobilized? First we review some cases of early visual processing where the mobilization of knowledge seems to be a key contributor to success yet where the knowledge is deliberately represented in a quite inflexible way. After considering the knowledge that is involved in overcoming the projective nature of images, we move the discussion to the knowledge that was required in programs to match, register, and recognize shapes in a range of applications. Finally, we discuss the current state of process architectures for knowledge mobilization.     

Phosphorylation of Hrs downstream of the epidermal growth factor receptor.

The hepatocyte growth factor-regulated tyrosine kinase substrate Hrs is an early endosomal protein that is thought to play a regulatory role in the trafficking of growth factor/receptor complexes through early endosomes. Stimulation of cells with epidermal growth factor (EGF) rapidly leads to phosphorylation of Hrs, raising the question whether the receptor tyrosine kinase phosphorylates Hrs directly. Here, we present evidence that a downstream kinase, rather than the active receptor kinase is responsible. We show that the nonreceptor tyrosine kinase Src is able to phosphorylate Hrs in vitro and in vivo, but that Hrs is nevertheless phosphorylated in Src-, Yes- and Fyn-negative cells. Moreover, we show that only 10-20% of Hrs is phosphorylated following EGF stimulation, and that phosphorylation occurs at multiple tyrosines located in different parts of Hrs. These results suggest that Hrs is a substrate for several kinases downstream of the EGF receptor.     

Evidence for the local evolution of mechanisms underlying limb regeneration in salamanders

The most extensive regenerative ability in adult vertebrates is found in the salamanders. Although it is often suggested that regeneration is an ancestral property for vertebrates, our studies on the cell-surface three-finger-protein Prod 1 provide clear evidence for the importance of local evolution of limb regeneration in salamanders. Prod 1 is implicated in both patterning and growth in the regeneration of limbs. It interacts with well-conserved proteins such as the epidermal growth-factor receptor and the anterior gradient protein that are widely expressed in phylogeny. A detailed analysis of the structure and sequence of Prod 1 in relation to other vertebrate three-finger proteins in mammals and zebra fish supports the view that it is a salamander-specific protein. This is the first example of a taxon-specific protein that is clearly implicated in the mechanisms of regeneration. We propose the hypothesis that regeneration depends on the activity of taxon-specific components in orchestrating a cellular machinery that is extensively conserved between regenerating and non-regenerating taxa. This hypothesis has significant implications for our outlook on regeneration in vertebrates, as well as for the strategies employed in extending regenerative ability in mammals.     

Polarity and form regulation in development and reconstitution

In the literature, it is often assumed, for example with respect to Hydra, that several Turing systems coexist and it is also assumed that maintaining the polar profile, even when the system increases in size, is important for the polarity of the final phenotype. It is shown here that in reality there is only one Turing system, Child's system. To obtain a complete polar individual or organ, whether in reconstitution or development, it is essential that the complete succession of metabolic patterns occurs. Child's concepts of physiological dominance, subordination and isolation are interpreted in the light of Turing theory and in particular the Turing wavelength. It is emphasised, particularly by pointing to Child's metabolic patterns in coelenterates, both in development and in reconstitution, that it is the elongation that drives the succession polar metabolic pattern-->bipolar metabolic pattern, and this corresponds to the prediction of Turing theory supporting the thesis that Child's metabolic pattern is a Turing pattern. It is shown that if we assume that ATP is the Turing inhibitor then the many results of Child about the reduction of the scale of organisation with the decrease in the intensity of the energy metabolism correspond to the reduction of the Turing wavelength. The interplay between the Turing wavelength and the length of the form explains the conditions of reconstitution under which partial forms, wholes and form regulation are obtained. It is suggested that higher metabolism is responsible for both larger size and larger Turing wavelength thus securing form regulation. The results could be of importance in modern 'regenerative biology'. Heteromorphosis, i.e. animals with two heads (or two tails), one at each end, is explained by a bipolar Turing-Child metabolic pattern replacing a polar metabolic pattern. This can be brought about by chemical or by genetic means and indeed the prediction for Drosophila that the transition, wild type-->Bicaudal D, occurs because a polar Turing pattern is replaced by bipolar Turing pattern is confirmed, again if we accept that Child's metabolic pattern is the underlying Turing pattern. Child's experiments on Drosophila, including the requirement of critical length for metabolic polarity, are explained by Turing theory. Phenocopies and phenotypes are explained by the Turing-Child theory. It is shown that both Child's results about metabolic patterns and modern results for Hydra about gap junctions, 'endogeneous inhibitor' and gene expression, are correlated and explained by (cAMP, ATP) Turing theory. It is argued that the double-gradient hypothesis is incorrect in its original formulation and that it is Child's conception of succeeding metabolic patterns that is the correct one and that it corresponds to the prediction of the Turing theory.     

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.     

Drosophila genes that affect meiosis duration are among the meiosis related genes that are more often found duplicated

Using a phylogenetic approach, the examination of 33 meiosis/meiosis-related genes in 12 Drosophila species, revealed nine independent gene duplications, involving the genes cav, mre11, meiS332, polo and mtrm. Evidence is provided that at least eight out of the nine gene duplicates are functional. Therefore, the rate at which Drosophila meiosis/meiosis-related genes are duplicated and retained is estimated to be 0.0012 per gene per million years, a value that is similar to the average for all Drosophila genes. It should be noted that by using a phylogenetic approach the confounding effect of concerted evolution, that is known to lead to overestimation of the duplication and retention rate, is avoided. This is an important issue, since even in our moderate size sample, evidence for long-term concerted evolution (lasting for more than 30 million years) was found for the meiS332 gene pair in species of the Drosophila subgenus. Most striking, in contrast to theoretical expectations, is the finding that genes that encode proteins that must follow a close stoichiometric balance, such as polo, mtrm and meiS332 have been found duplicated. The duplicated genes may be examples of gene neofunctionalization. It is speculated that meiosis duration may be a trait that is under selection in Drosophila and that it has different optimal values in different species.     

Polo-like kinase-1 controls recovery from a G2 DNA damage-induced arrest in mammalian cells

DNA damage triggers multiple checkpoint pathways to arrest cell cycle progression. Less is known about the mechanisms that allow resumption of the cell cycle once checkpoint signaling is silenced. Here we show that while in undamaged cells several redundant pathways can promote the onset of mitosis, this redundancy is lost in cells recovering from a DNA damage-induced arrest. We demonstrate that Plk1 is crucial for mitotic entry following recovery from DNA damage. However, Plk1 is no longer required in cells depleted of Wee1, and we could show that Plk1 is involved in the degradation of Wee1 at the onset of mitosis. Thus, our data show that the cell cycle machinery is reset in response to DNA damage and that cells become critically dependent on Plk1-mediated degradation of Wee1 for their recovery.     

ch-TOGp is required for microtubule aster formation in a mammalian mitotic extract

Microtubules induced to polymerize with taxol in a mammalian mitotic extract organize into aster-like arrays in a centrosome-independent process that is driven by microtubule motors and structural proteins. These microtubule asters accurately reflect the noncentrosomal aspects of mitotic spindle pole formation. We show here that colonic-hepatic tumor-overexpressed gene (ch-TOGp) is an abundant component of these asters. We have prepared ch-TOGp-specific antibodies and show by immunodepletion that ch-TOGp is required for microtubule aster assembly. Microtubule polymerization is severely inhibited in the absence of ch-TOGp, and silver stain analysis of the ch-TOGp immunoprecipitate indicates that it is not present in a preformed complex and is the only protein removed from the extract during immunodepletion. Furthermore, the reduction in microtubule polymerization efficiency in the absence of ch-TOGp is dependent on ATP. These results demonstrate that ch-TOGp is a major constituent of microtubule asters assembled in a mammalian mitotic extract and that it is required for robust microtubule polymerization in an ATP-dependent manner in this system even though taxol is present. These data, coupled with biochemical and genetic data derived from analysis of ch-TOGp-related proteins in other organisms, indicate that ch-TOGp is a key factor regulating microtubule dynamics during mitosis.