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.     

Hybrid tetramers reveal elements of cooperativity in Escherichia coli D-3-phosphoglycerate dehydrogenase

d-3-Phosphoglycerate dehydrogenase from Escherichia coli is a tetramer of identical subunits that is inhibited when l-serine binds at allosteric sites between subunits. Co-expression of two genes, the native gene containing a charge difference mutation and a gene containing a mutation that eliminates serine binding, produces hybrid tetramers that can be separated by ion exchange chromatography. Activity in the hybrid tetramer with only a single intact serine binding site is inhibited by approximately 58% with a Hill coefficient of 1. Thus, interaction at a single regulatory domain interface does not, in itself, lead to the positive cooperativity of inhibition manifest in the native enzyme. Tetramers with only two intact serine binding sites purify as a mixture that displays a maximum inhibition level that is less than that of native enzyme, suggesting the presence of a population of tetramers that are unable to be fully inhibited. Differential analysis of this mixture supports the conclusion that it contains two forms of the tetramer. One form contains two intact serine binding sites at the same interface and is not fully inhibitable. The second form is a fully inhibitable population that has one serine binding site at each interface. Overall, the hybrid tetramers show that the positive cooperativity observed for serine binding is mediated across the nucleotide binding domain interface, and the negative cooperativity is mediated across the regulatory domain interface. That is, they reveal a pattern in which the binding of serine at one interface leads to negative cooperativity of binding of a subsequent serine at the same interface and positive cooperativity of binding of a subsequent serine to the opposite interface. This trend is propagated to subsequent binding sites in the tetramer such that the negative cooperativity that is originally manifest at one interface is decreased by subsequent binding of ligand at the opposite interface.     

Evidence for a role of a tumor necrosis factor-alpha (TNF-alpha)-converting enzyme-like protease in shedding of TRANCE, a TNF family member involved in osteoclastogenesis and dendritic cell survival

Tumor necrosis factor (TNF)-related activation-induced cytokine (TRANCE), a member of the TNF family, is a dendritic cell survival factor and is essential for osteoclastogenesis and osteoclast activation. In this report we demonstrate (i) that TRANCE, like TNF-alpha, is made as a membrane-anchored precursor, which is released from the plasma membrane by a metalloprotease; (ii) that soluble TRANCE has potent dendritic cell survival and osteoclastogenic activity; (iii) that the metalloprotease-disintegrin TNF-alpha convertase (TACE) can cleave immunoprecipitated TRANCE in vitro in a fashion that mimics the cleavage observed in tissue culture cells; and (iv) that in vitro cleavage of a TRANCE ectodomain/CD8 fusion protein and of a peptide corresponding to the TRANCE cleavage site by TACE occurs at the same site that is used when TRANCE is shed from cells into the supernatant. We propose that the TRANCE ectodomain is released from cells by TACE or a related metalloprotease-disintegrin, and that this release is an important component of the function of TRANCE in bone and immune homeostasis.     

ON THE INFLUENCE OF AGGREGATES ON THE MEMBRANE POTENTIALS AND THE OSMOTIC PRESSURE OF PROTEIN SOLUTIONS

1. It is shown that when part of the gelatin in a solution of gelatin chloride is replaced by particles of powdered gelatin (without change of pH) the membrane potential of the solution is influenced comparatively little. 2. A measurement of the hydrogen ion concentration of the gelatin chloride solution and the outside aqueous solution with which the gelatin solution is in osmotic equilibrium, shows that the membrane potential can be calculated from this difference of hydrogen ion concentration with an accuracy of half a millivolt. This proves that the membrane potential is due to the establishment of a membrane equilibrium and that the powdered particles participate in this membrane equilibrium. 3. It is shown that a Donnan equilibrium is established between powdered particles of gelatin chloride and not too strong a solution of gelatin chloride. This is due to the fact that the powdered gelatin particles may be considered as a solid solution of gelatin with a higher concentration than that of the weak gelatin solution in which they are suspended. It follows from the theory of membrane equilibria that this difference in concentration of protein ions must give rise to potential differences between the solid particles and the weaker gelatin solution. 4. The writer had shown previously that when the gelatin in a solution of gelatin chloride is replaced by powdered gelatin (without a change in pH), the osmotic pressure of the solution is lowered the more the more dissolved gelatin is replaced by powdered gelatin. It is therefore obvious that the powdered particles of gelatin do not participate in the osmotic pressure of the solution in spite of the fact that they participate in the establishment of the Donnan equilibrium and in the membrane potentials. 5. This paradoxical phenomenon finds its explanation in the fact that as a consequence of the participation of each particle in the Donnan equilibrium, a special osmotic pressure is set up in each individual particle of powdered gelatin which leads to a swelling of that particle, and this osmotic pressure is measured by the increase in the cohesion pressure of the powdered particles required to balance the osmotic pressure inside each particle. 6. In a mixture of protein in solution and powdered protein (or protein micellæ) we have therefore two kinds of osmotic pressure, the hydrostatic pressure of the protein which is in true solution, and the cohesion pressure of the aggregates. Since only the former is noticeable in the hydrostatic pressure which serves as a measure of the osmotic pressure of a solution, it is clear why the osmotic pressure of a protein solution must be diminished when part of the protein in true solution is replaced by aggregates.     

A mechanism for exact sensory adaptation based on receptor modification

We provide a theoretical explanation for the observation that in many sensory systems a step increase in stimulus triggers a response that goes through a maximum and then returns to the basal level. Considered here is a receptor molecule that in the absence of ligand can be found in either of two states R and D. Two more states, RL and DL, are formed upon the addition of ligand L. It is assumed that the receptor triggers activity in a sensory system, and that the activity is proportional to a weighted combination of the fractions of molecules that are in each of the four states. It is shown that judicious choice of the weights can provide both an adequate response and exact adaptation to step increases in stimuli. The interconversion between states may operate without energy expenditure or through covalent modification. In both cases, adaptation is associated with receptor modification that acts as a counterweight to changed external conditions. Application to cAMP secretion in Dictyostelium discoideum and to chemotaxis in bacteria is discussed.     

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.     

The problem of counting sites in the estimation of the synonymous and nonsynonymous substitution rates: implications for the correlation between the synonymous substitution rate and codon usage bias

Most methods for estimating the rate of synonymous and nonsynonymous substitution per site define a site as a mutational opportunity: the proportion of sites that are synonymous is equal to the proportion of mutations that would be synonymous under the model of evolution being considered. Here we demonstrate that this definition of a site can give misleading results and that a physical definition of site should be used in some circumstances. We illustrate our point by reexamining the relationship between codon usage bias and the synonymous substitution rate. It has recently been shown that the rate of synonymous substitution, calculated using the Goldman-Yang method, which encapsulates the mutational-opportunity definition of a site at a high level of sophistication, is either positively correlated or uncorrelated to synonymous codon bias in Drosophila. Using other methods, which account for synonymous codon bias but define a site physically, we show that there is a negative correlation between the synonymous substitution rate and codon bias and that the lack of a negative correlation using the Goldman-Yang method is due to the way in which the number of synonymous sites is counted. We also show that there is a positive correlation between the synonymous substitution rate and third position GC content in mammals, but that the relationship is considerably weaker than that obtained using the Goldman-Yang method. We argue that the Goldman-Yang method is misleading in this context and conclude that methods that rely on a mutational-opportunity definition of a site should be used with caution.     

Molecular characterization of CTNS deletions in nephropathic cystinosis: development of a PCR-based detection assay.

Nephropathic cystinosis is an autosomal recessive disorder that is characterized by accumulation of intralysosomal cystine and is caused by a defect in the transport of cystine across the lysosomal membrane. Using a positional cloning strategy, we recently cloned the causative gene, CTNS, and identified pathogenic mutations, including deletions, that span the cystinosis locus. Two types of deletions were detected-one of 9.5-16 kb, which was seen in a single family, and one of approximately 65 kb, which is the most frequent mutation found in the homozygous state in nearly one-third of cystinotic individuals. We present here characterization of the deletion breakpoints and demonstrate that, although both deletions occur in regions of repetitive sequences, they are the result of nonhomologous recombination. This type of mechanism suggests that the approximately 65-kb deletion is not a recurrent mutation, and our results confirm that it is identical in all patients. Haplotype analysis shows that this large deletion is due to a founder effect that occurred in a white individual and that probably arose in the middle of the first millenium. We also describe a rapid PCR-based assay that will accurately detect both homozygous and heterozygous deletions, and we use it to show that the approximately 65-kb deletion is present in either the homozygous or the heterozygous state in 76% of cystinotic patients of European origin.     

Copper toxicity in Alzheimer's disease: cognitive loss from ingestion of inorganic copper

In this review I present the hypothesis that a toxic substance, inorganic copper, ingested from drinking water and vitamin/mineral supplements containing inorganic copper, is at least partially causal of the epidemic of Alzheimer's disease (AD) we are seeing in developed countries. I set the stage for this hypothesis by pointing out that the epidemic is a new disease phenomenon coinciding temporally with the use of copper plumbing in developed countries. The evidence is good that AD was nonexistent or rare in the 1800 s and early 1900 s, and the arguments that elderly people did not exist in those times, or that AD was simply attributed to senility, are refuted. The web of evidence tying ingestion of inorganic copper as a causal factor in AD is strong, and includes AD animal model data where trace amounts of inorganic copper in the drinking water markedly worsened AD, human studies where ingestion of copper supplements, along with a high fat diet, is associated with a marked loss of cognition, human studies showing a markedly higher mortality in elderly women ingesting copper supplements, as well as other data. It is likely that a high fat diet works in conjunction with ingestion of inorganic copper to increase the risk of AD. It is clear that some factor toxic to the brain is present in the environment in developed countries, but not undeveloped countries, and is a major risk factor for AD. I believe that that toxic factor is ingestion of inorganic copper.     

Does Computation Reveal Machine Cognition?

This paper seeks to understand machine cognition. The nature of machine cognition has been shrouded in incomprehensibility. We have often encountered familiar arguments in cognitive science that human cognition is still faintly understood. This paper will argue that machine cognition is far less understood than even human cognition despite the fact that a lot about computer architecture and computational operations is known. Even if there have been putative claims about the transparency of the notion of machine computations, these claims do not hold out in unraveling machine cognition, let alone machine consciousness (if there is any such thing). The nature and form of machine cognition remains further confused also because of attempts to explain human cognition in terms of computation and to model/simulate (aspects of) human cognitive processing in machines. Given that these problems in characterizing machine cognition persist, a view of machine cognition that aims to avoid these problems is outlined. The argument that is advanced is that something becomes a computation in machines only when a human interprets it, which is a kind of semiotic causation. From this it follows that a computing machine is not engaged in a computation unless a human interprets what it is doing; instead, it is engaged in machine cognition, which is defined as a member or subset of the set of all possible mappings of inputs to outputs. The human interpretation, which is a semiotic process, gives meaning to what a machine does, and then what it does becomes a computation.     

Calmodulin bound to the first IQ motif is responsible for calcium-dependent regulation of myosin 5a

Myosin 5a is as yet the best-characterized unconventional myosin motor involved in transport of organelles along actin filaments. It is well-established that myosin 5a is regulated by its tail in a Ca(2+)-dependent manner. The fact that the actin-activated ATPase activity of myosin 5a is stimulated by micromolar concentrations of Ca(2+) and that calmodulin (CaM) binds to IQ motifs of the myosin 5a heavy chain indicates that Ca(2+) regulates myosin 5a function via bound CaM. However, it is not known which IQ motif and bound CaM are responsible for the Ca(2+)-dependent regulation and how the head-tail interaction is affected by Ca(2+). Here, we found that the CaM in the first IQ motif (IQ1) is responsible for Ca(2+) regulation of myosin 5a. In addition, we demonstrate that the C-lobe fragment of CaM in IQ1 is necessary for mediating Ca(2+) regulation of myosin 5a, suggesting that the C-lobe fragment of CaM in IQ1 participates in the interaction between the head and the tail. We propose that Ca(2+) induces a conformational change of the C-lobe of CaM in IQ1 and prevents interaction between the head and the tail, thus activating motor function.     

Epitope-tagged ubiquitin. A new probe for analyzing ubiquitin function.

In the present work, a method based on an epitope-tagged ubiquitin derivative is described that allows for the unambiguous detection of ubiquitin-protein conjugates formed in vivo or in vitro. Expression in the yeast Saccharomyces cerevisiae of ubiquitin that has been tagged at its amino terminus with a peptide epitope results in the formation of tagged ubiquitin-protein conjugates that are detectable by immunoblotting with a monoclonal antibody that recognizes the tag. The expression of tagged ubiquitin has no adverse effect on vegetative growth and, moreover, can suppress the stress-hypersensitive phenotype of yeast lacking the polyubiquitin gene UBI4. We also show that tagged ubiquitin is correctly conjugated in vivo and in vitro to a short-lived test protein and can be covalently extended into the multimeric ubiquitin chain that is normally required for the degradation of this protein. Surprisingly, however, conjugation of tagged ubiquitin inhibits proteolysis. These and related results suggest that the amino-terminal region of ubiquitin is important in protease-substrate recognition and that the multiubiquitin chain is a dynamic transient structure. The potential of tagged ubiquitin for the identification and isolation of ubiquitin-protein conjugates and ubiquitin-related enzymes, and as a tool in mechanistic studies is discussed.     

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.     

Implications of the gene balance hypothesis for dosage compensation

Dosage compensation refers to the equal expression between the sexes despite the fact that the dosage of the X chromosome is different in males and females. In Drosophila there is a twofold upregulation of the single male X. In triple X metafemales, there is also dosage compensation, which occurs by a two-thirds downregulation. There is a concomitant reduction in expression of many autosomal genes in metafemales. The male specific lethal (MSL) complex is present on the male X chromosome. Evidence is discussed showing that the MSL complex sequesters a histone acetyltransferase to the X chromosome to mute an otherwise increased expression by diminishing the histone acetylation on the autosomes. Several lines of evidence indicate that a constraining activity occurs from the MSL complex to prevent overcompensation on the X that might otherwise occur from the high level of acetylation present. Together, the evidence suggests that dosage compensation is a modification of a regulatory inverse dosage effect that is a reflection of intrinsic gene regulatory mechanisms and that the MSL complex has evolved in reaction in order to equalize the expression on both the X and autosomes of males and females.     

Staphylococcus intermedius produces a functional agr autoinducing peptide containing a cyclic lactone

The agr system is a global regulator of accessory functions in staphylococci, including genes encoding exoproteins involved in virulence. The agr locus contains a two-component signal transduction module that is activated by an autoinducing peptide (AIP) encoded within the agr locus and is conserved throughout the genus. The AIP has an unusual partially cyclic structure that is essential for function and that, in all but one case, involves an internal thiolactone bond between a conserved cysteine and the C-terminal carboxyl group. The exceptional case is a strain of Staphylococcus intermedius that has a serine in place of the conserved cysteine. We demonstrate here that the S. intermedius AIP is processed by the S. intermedius AgrB protein to generate a cyclic lactone, that it is an autoinducer as well as a cross-inhibitor, and that all of five other S. intermedius strains examined also produce serine-containing AIPs.     

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.