Recognition principle of the TAP transporter disclosed by combinatorial peptide libraries

Transport of peptides across the membrane of the endoplasmic reticulum for assembly with MHC class I molecules is an essential step in antigen presentation to cytotoxic T cells. This task is performed by the major histocompatibility complex-encoded transporter associated with antigen processing (TAP). Using a combinatorial approach we have analyzed the substrate specificity of human TAP at high resolution and in the absence of any given sequence context, revealing the contribution of each peptide residue in stabilizing binding to TAP. Human TAP was found to be highly selective with peptide affinities covering at least three orders of magnitude. Interestingly, the selectivity is not equally distributed over the substrate. Only the N-terminal three positions and the C-terminal residue are critical, whereas effects from other peptide positions are negligible. A major influence from the peptide backbone was uncovered by peptide scans and libraries containing d amino acids. Again, independent of peptide length, critical positions were clustered near the peptide termini. These approaches demonstrate that human TAP is selective, with residues determining the affinity located in distinct regions, and point to the role of the peptide backbone in binding to TAP. This binding mode of TAP has implications in an optimized repertoire selection and in a coevolution with the major histocompatibility complex/T cell receptor complex.

Invariance between subjects of brain wave representations of language

In three experiments, electric brain waves of 19 subjects were recorded under several different experimental conditions for two purposes. One was to test how well we could recognize which sentence, from a set of 24 or 48 sentences, was being processed in the cortex. The other was to study the invariance of brain waves between subjects. As in our earlier work, the analysis consisted of averaging over trials to create prototypes and test samples, to both of which Fourier transforms were applied, followed by filtering and an inverse transformation to the time domain. A least-squares criterion of fit between prototypes and test samples was used for classification. In all three experiments, averaging over subjects improved the recognition rates. The most significant finding was the following. When brain waves were averaged separately for two nonoverlapping groups of subjects, one for prototypes and the other for test samples, we were able to recognize correctly 90% of the brain waves generated by 48 different sentences about European geography.

Invariance of brain-wave representations of simple visual images and their names

In two experiments, electric brain waves of 14 subjects were recorded under several different conditions to study the invariance of brain-wave representations of simple patches of colors and simple visual shapes and their names, the words blue, circle, etc. As in our earlier work, the analysis consisted of averaging over trials to create prototypes and test samples, to both of which Fourier transforms were applied, followed by filtering and an inverse transformation to the time domain. A least-squares criterion of fit between prototypes and test samples was used for classification. The most significant results were these. By averaging over different subjects, as well as trials, we created prototypes from brain waves evoked by simple visual images and test samples from brain waves evoked by auditory or visual words naming the visual images. We correctly recognized from 60% to 75% of the test-sample brain waves. The general conclusion is that simple shapes such as circles and single-color displays generate brain waves surprisingly similar to those generated by their verbal names. These results, taken together with extensive psychological studies of auditory and visual memory, strongly support the solution proposed for visual shapes, by Bishop Berkeley and David Hume in the 18th century, to the long-standing problem of how the mind represents simple abstract ideas.

A resource range invariance rule for optimal offspring size predicts patterns of variability in parental phenotypes

Previous analysis of the rules regarding how much more a female should invest in a litter of size C rather than producing a litter with one more offspring revealed an invariance relationship between litter size and the range of resources per offspring in any litter size. The rule is that the range of resources per offspring should be inversely proportional to litter size. Here we present a modification of this rule that relates litter size to the total resources devoted to reproduction at that litter size. The result is that the range of resources devoted to reproduction should be the same for all litter sizes. When parental phenotypes covary linearly with resources devoted to reproduction, then those traits should also show equal ranges within each litter size category (except for litters of one). We tested this prediction by examining the range in body size (=total length) of female mosquito fish (Gambusia hubbsi) at different litter sizes. Because resources devoted to reproduction may take many forms (e.g., nest defense), this prediction may have broad applicability.

Structural invariance of constitutively active and inactive mutants of Acanthamoeba myosin IC bound to F-actin in the rigor and ADP-bound states

The three single-headed monomeric myosin I isozymes of Acanthamoeba castellanii (AMIs)—AMIA, AMIB, and AMIC—are among the best-studied of all myosins. We have used AMIC to study structural correlates of myosin’s actin-activated ATPase. This activity is normally controlled by phosphorylation of Ser-329, but AMIC may be switched into constitutively active or inactive states by substituting this residue with Glu or Ala, respectively. To determine whether activation status is reflected in structural differences in the mode of attachment of myosin to actin, these mutant myosins were bound to actin filaments in the absence of nucleotide (rigor state) and visualized at 24-Å resolution by using cryoelectron microscopy and image reconstruction. No such difference was observed. Consequently, we suggest that regulation may be affected not by altering the static (time-averaged) structure of AMIC but by modulating its dynamic properties, i.e., molecular breathing. The tail domain of vertebrate intestinal brush-border myosin I has been observed to swing through 31° on binding of ADP. However, it was predicted on grounds of differing kinetics that any such effects with AMIC should be small [Jontes, J. D., Ostap, E. M., Pollard, T. D. & Milligan, R. A. (1998) J. Cell Biol. 141, 155–162]. We have confirmed this hypothesis by observing actin-associated AMIC in its ADP-bound state. Finally, we compared AMIC to brush-border myosin I and AMIB, which were previously studied under similar conditions. In each case, the shape and angle of attachment to F-actin of the catalytic domain is largely conserved, but the domain structure and disposition of the tail is distinctively different for each myosin.

The hard-soft acid-base principle in enzymatic catalysis: dual reactivity of phosphoenolpyruvate.

In this paper, the chemical reactivity of C3 of phosphoenolpyruvate (PEP) has been analyzed in terms of density functional theory quantified through quantum chemistry calculations. PEP is involved in a number of important enzymatic reactions, in which its C3 atom behaves like a base. In three different enzymatic reactions analyzed here, C3 sometimes behaves like a soft base and sometimes behaves like a hard base in terms of the hard-soft acid-base principle. This dual nature of C3 of PEP was found to be related to the conformational change of the molecule. This leads to a testable hypothesis: that PEP adopts particular conformations in the enzyme-substrate complexes of different PEP-using enzymes, and that the enzymes control the reactivity through controlling the dihedral angle between the carboxylate and the C==C double bond of PEP.

The resource consumption principle: attention and memory in volumes of neural tissue.

In the cerebral cortex, the small volume of the extracellular space in relation to the volume enclosed by synapses suggests an important functional role for this relationship. It is well known that there are atoms and molecules in the extracellular space that are absolutely necessary for synapses to function (e.g., calcium). I propose here the hypothesis that the rapid shift of these atoms and molecules from extracellular to intrasynaptic compartments represents the consumption of a shared, limited resource available to local volumes of neural tissue. Such consumption results in a dramatic competition among synapses for resources necessary for their function. In this paper, I explore a theory in which this resource consumption plays a critical role in the way local volumes of neural tissue operate. On short time scales, this principle of resource consumption permits a tissue volume to choose those synapses that function in a particular context and thereby helps to integrate the many neural signals that impinge on a tissue volume at any given moment. On longer time scales, the same principle aids in the stable storage and recall of information. The theory provides one framework for understanding how cerebral cortical tissue volumes integrate, attend to, store, and recall information. In this account, the capacity of neural tissue to attend to stimuli is intimately tied to the way tissue volumes are organized at fine spatial scales.

Invariance and restriction toward a limited set of self-antigens characterize neonatal IgM antibody repertoires and prevail in autoreactive repertoires of healthy adults.

Analysis of the reactivity of IgM with self-antigens in tissues by a quantitative immunoblotting technique showed striking invariance among newborns in the human and in the mouse. The self-reactive repertoire of IgM of adults was also markedly conserved; it comprised most anti-self reactivities that prevailed among neonates. Multivariate analysis confirmed the homogeneity of IgM repertoires of neonates toward self- and non-self-antigens. Multivariate analysis discriminated between newborn and adult repertoires for reactivity with two of five sources of self-proteins and with non-self-antigens. Our observations support the concept that naturally activated B lymphocytes are selected early in development and throughout life for reactivity with a restricted set of self-antigens.

Groups, information theory, and Einstein's likelihood principle

We propose a unifying picture where the notion of generalized entropy is related to information theory by means of a group-theoretical approach. The group structure comes from the requirement that an entropy be well defined with respect to the composition of independent systems, in the context of a recently proposed generalization of the Shannon-Khinchin axioms. We associate to each member of a large class of entropies a generalized information measure, satisfying the additivity property on a set of independent systems as a consequence of the underlying group law. At the same time, we also show that Einstein's likelihood function naturally emerges as a byproduct of our informational interpretation of (generally nonadditive) entropies. These results confirm the adequacy of composable entropies both in physical and social science contexts.

Coverage and invariance for the biological control of pests in mediterranean greenhouses

A major problem related to the treatment of ecosystems is that they have no available mathematical formalization. This implies that many of their properties are not presented as short, rigorous modalities, but rather as long expressions which, from a biological standpoint, totally capture the significance of the property, but which have the disadvantage of not being sufficiently manageable, from a mathematical standpoint. The interpretation of ecosystems through networks allows us to employ the concepts of coverage and invariance alongside other related concepts. The latter will allow us to present the two most important relations in an ecosystem – predator–prey and competition – in a different way. Biological control, defined as “the use of living organisms, their resources or their products to prevent or reduce loss or damage caused by pests”, is now considered the environmentally safest and most economically advantageous method of pest control (van Lenteren, 2011). A guild includes all those organisms that share a common food resource (Polis et al., 1989), which in the context of biological control means all the natural enemies of a given pest. There are several types of intraguild interactions, but the one that has received most research attention is intraguild predation, which occurs when two organisms share the same prey while at the same time participating in some kind of trophic interaction. However, this is not the only intraguild relationship possible, and studies are now being conducted on others, such as oviposition deterrence. In this article, we apply the developed concepts of structural functions, coverage, invariant sets, etc. (Lloret et al., 1998, Esteve and Lloret, 2006a, Esteve and Lloret, 2006b and Esteve and Lloret, 2007) to a tritrophic system that includes aphids, one of the most damaging pests and a current bottleneck for the success of biological control in Mediterranean greenhouses.

School Anxiety Inventory–Short Version: Factorial Invariance and Latent Mean Differences Across Gender and Age in Spanish Adolescents

This study examined the factorial invariance and latent mean differences of the School Anxiety Inventory–Short Version across gender and age groups for 2,367 Spanish students, ranging in age from 12 to 18 years. Configural and measurement invariance were found across gender and age samples for all dimensions of the School Anxiety Inventory–Short Version.

On the Result of Invariance of the Closure Set of the Real Projections of the Zeros of an Important Class of Exponential Polynomials

In this paper we provide the proof of a practical point-wise characterization of the set RP defined by the closure set of the real projections of the zeros of an exponential polynomial P(z) = Σn j=1 cjewjz with real frequencies wj linearly independent over the rationals. As a consequence, we give a complete description of the set RP and prove its invariance with respect to the moduli of the c′ js, which allows us to determine exactly the gaps of RP and the extremes of the critical interval of P(z) by solving inequations with positive real numbers. Finally, we analyse the converse of this result of invariance.