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Genetic control of the T-lymphocyte proliferative response to cytochrome c.

Cytochromes c have been used as antigens in a murine T-lymphocyte proliferation assay in order to characterize the nature of determinants whose recognition is under immune response (Ir) gene control. The cytochromes are advantagous as antigens because 1) they have well-characterized primary and tertiary structures, 2) they are antigenically simple, differing from mouse cytochrome c at only a small number of amino acid residues, and 3) there exist a large number of evolutionary variants which can be used to locate antigenic sites by cross-stimulation. In the present studies, the T-lymphocyte proliferative response to pigeon cytochrome c was shown to be under the control of two complementing major histocompatibility (MHC)-linked Ir genes in mice of the H-2a and H-2k haplotypes. Mice of the H-2b, H-2d, H-2p, H-2q, H-2s, and H-2u haplotypes were low or nonresponders. Complementation was demonstrated by showing that an F1 hybrid between two nonresponder recombinant strains, B10.A(4R) and B10.A(5R), could respond to pigeon cytochrome c. The determinant on the cytochrome recognized in this immune response was located to the C-terminal portion of the molecule around residues 89 and/or 100. This was shown by the failure of closely related cytochromes from the Pekin duck and chicken to cross-stimulate T lymphocytes immune to pigeon cytochrome; position 89 and 100 carry the only residues different from those in mouse cytochrome c that are unique to pigeon cytochrome among the three bird cytochromes tested. This localization was further substantiated by demonstrating that the cyanogen bromide cleavage-fragment (residues 81-104) from pigeon cytochrome, but not the same fragment from Pekin duck cytochrome, was as good a stimulant of T cells immune to the whole molecule as the intact cytochrome. These results identify the immunogenic site on the molecule as one which differs from mouse cytochrome c by only one or two amino-acid residues. Thus, T-cell immune responses, which are under MHC-linked Ir gene control, are as capable as antibody responses of recognizing subtle differences in protein structure. However, the ability of T cells to respond equally well to stimulation with polypeptide fragments or with the whole molecule suggests either that T-cell recognition involves certain differences from B cell recognition or that in some cases the fragments possess a similar spatial structure to that of the corresponding segment in the native protein.

Animals↗

Heterotrophic bacteria in water distribution systems. I. Spatial and temporal variation.

The drinking water distribution system of the city of Metz in France was sampled intensively during six, monthly surveys which were designed to determine the spatial and temporal distribution of total heterotrophic bacteria in the network. A non-hierarchical nearest-centroid clustering method was used for dividing the water distribution system into zones corresponding to different levels of bacterial density. The general pattern of the spatial heterogeneity showed a high degree of reproducibility. Since the frequency distribution of total heterotrophic bacteria within the zones was compatible with the negative binomial distribution, the water distribution system studied may be considered as being composed of several heterogeneous subsystems. The consistency of this structured spatial dispersion pattern of bacteria in light of some physical and chemical characteristics of the system is evident. In consideration of the principal features of flow in the system relevant to the layout of water mains, the location of zones of highest bacterial concentrations have been attributed to lower levels of chlorine residuals and prolonged retention time of the water in the network, especially in the storage units, before reaching the various distribution areas. Although the monthly variation in the bacterial concentration of the entire system showed a marked increase which was concomitant with warmest water temperatures, the zones were subject to noticeable discrepancies in the range of temporal variation.

Bacteria↗

Folding stabilizes the evolution of catalysts.

Sequence folding is known to determine the spatial structure and catalytic function of proteins and nucleic acids. We show here that folding also plays a key role in enhancing the evolutionary stability of the intermolecular recognition necessary for the prevalent mode of catalytic action in replication, namely, in trans, one molecule catalyzing the replication of another copy, rather than itself. This points to a novel aspect of why molecular life is structured as it is, in the context of life as it could be: folding allows limited, structurally localized recognition to be strongly sensitive to global sequence changes, facilitating the evolution of cooperative interactions. RNA secondary structure folding, for example is shown to be able to stabilize the evolution of prolonged functional sequences, using only a part of this length extension for intermolecular recognition, beyond the limits of the (cooperative) error threshold. Such folding could facilitate the evolution of polymerases in spatially heterogeneous systems. This facilitation is, in fact, vital because physical limitations prevent complete sequence-dependent discrimination for any significant-size biopolymer substrate. The influence of partial sequence recognition between biopolymer catalysts and complex substrates is investigated within a stochastic, spatially resolved evolutionary model of trans catalysis. We use an analytically tractable nonlinear master equation formulation called PRESS (McCaskill et al., Biol. Chem. 382: 1343-1363), which makes use of an extrapolation of the spatial dynamics down from infinite dimensional space, and compare the results with Monte Carlo simulations.

Catalysis↗

[Hydrogen-bond state analysis of cellobiohydrolase I molecule from Trichoderma viride].

Hydrogen-bond states on cellobiohydrolase II (CBH II) of Trichoderma viride were analysed by laser Raman spectroscopic method used to reveal molecular normal modes of vibration character. The results indicated that hydrogen-bond ability of carbonyl oxygen-atom of amide I was raised in two types of aqueous solution samples (6.0 and 8.0 of pH value) compared to the solid sample. The variation trend of beta structure modes was similar between amide II and amide I. As far as the ability of hydrogen-bond forming is concerned, tryptophan (Trp) and tyrosine (Typ) residues are strong hydrogen proton donor in pH 6.0 and solid sample, thus proving the results of previously spatial structure analysis. By analysis of free S-H character, the -S-S- construction in Trichoderma viride mature peptide has been proved to be the same as that of Trichoderma reesei.

Cellulose 1,4-beta-Cellobiosidase↗

Spatial and temporal variation in the infestation of sea trout (Salmo trutta L.) by the caligid copepod Lepeophtheirus salmonis (Krøyer) in relation to sources of infection in Ireland.

Infestations of post-smolt sea trout (Salmo trutta L.) by the salmon louse (Lepeophtheirus salmonis Krøyer) were characterized in 42 estuaries over a 5 year period in Ireland. Spatial variation in infestation was more significant than temporal trends and existed at 3 levels; between regions (regions > 100 km of coastline), between bays within regions (bays < 50 km in length) and between estuaries within bays (distance between estuaries < 10 km). The observed spatial structure in infestations inferred that production of the infective larvae varied between regions and bays and that there was limited movement of fish and infective larvae between regions and bays. In addition the different levels of infestation recorded between estuaries in the same bay indicated short spatial scale variability in parasite transmission. Significantly higher infestations occurred in bays that contained lice-infested farmed salmon. Lice-infested wild spring salmon, which were present in estuaries of some systems, did not have a significant positive impact on infestations.

Analysis of Variance↗

Compound library development guided by protein structure similarity clustering and natural product structure.

To identify biologically relevant and drug-like protein ligands for medicinal chemistry and chemical biology research the grouping of proteins according to evolutionary relationships and conservation of molecular recognition is an established method. We propose to employ structure similarity clustering of the ligand-sensing cores of protein domains (PSSC) in conjunction with natural product guided compound library development as a synergistic approach for the identification of biologically prevalidated ligands with high fidelity. This is supported by the concepts that (i) in nature spatial structure is more conserved than amino acid sequence, (ii) the number of fold types characteristic for all protein domains is limited, and (iii) the underlying frameworks of natural product classes with multiple biological activities provide evolutionarily selected starting points in structural space. On the basis of domain core similarity considerations and irrespective of sequence similarity, Cdc25A phosphatase, acetylcholinesterase, and 11beta-hydroxysteroid dehydrogenases type 1 and type 2 were grouped into a similarity cluster. A 147-member compound collection derived from the naturally occurring Cdc25A inhibitor dysidiolide yielded potent and selective inhibitors of the other members of the similarity cluster with a hit rate of 2-3%. Protein structure similarity clustering may provide an experimental opportunity to identify supersites in proteins.

11-beta-Hydroxysteroid Dehydrogenases↗

Analysis of spatial patterns at a geographical scale over north-western Europe from point-referenced aphid count data.

The spatial analysis by distance indices (SADIE) technique was developed to evaluate the spatial pattern of point-referenced count data as well as the spatial association between two sets of data sharing the same point locations. This paper presents an analysis of spatial patterns in aphid count data and the association of these data with climate across north-west Europe. The paper tests the applicability of the technique to large geographical areas. Aggregation and cluster indices were calculated for the total annual abundance of the peach-potato aphid Myzus persicae (Sulzer) and for the annual mean rainfall and temperature at aphid monitoring sites. Association indices demonstrated the stability in time of aphid spatial structures and the correlation between aphid density and climate patterns. Groups of relatively large numbers of aphids, termed patches, and groups of relatively small numbers of aphids, termed gaps, were located and their mean size estimated. The aphid patterns were quite stable in time and the spatial patterns of temperature and rainfall were weakly associated with M. persicae annual abundance. Similarities were observed between the results of SADIE and those from the more widely used technique of spatial autocorrelation (SAC). However, the SADIE association index has the advantage of quantifying the possible associations between aphid data and the factors that determine population distribution. Thus, high temperature and low rainfall were identified as environmental factors that were positively associated with aphid abundance across north-west Europe.

Animals↗

[Spatial distribution pattern and space dependence of Contarinia sp. and Erigonidium graminicola in jujube orchard].

With the principles and methodologies of geostatistics, this paper studied the spatial structure and space dependence of Contarinia sp. and its natural enemy Erigonidium graminicola in a jujube orchard at different date. The results indicated that the semivariogram of Contarinia sp. on 8 June, 27 August and 19 October could be described by spherical model, showing an aggregated spatial distribution with the ranges of spatial dependence being 26.3, 7.8 and 22.0 m, and the degrees of spatial dependence being 88.05%, 85.77% and 87.58%, respectively. The semivariogram of Erigonidium graminicola could be also described by spherical model, showing an aggregated distribution with the ranges of spatial dependence being 28.3, 22.5 and 22.2 m, and the degrees of spatial dependence being 90.09%, 87.96% and 85.72%, respectively. It is suggested that Erigonidium graminicola is the dominant natural enemy against Contarinia sp. population in the examined jujube orchard.

Animals↗

Intra metropolitan demographic structure: a Seattle example.

"Internal urban variation in demographic character (births, deaths, fertility, natural increase, net migration) is analyzed in relation to age of persons, age of housing, ownership, distance from the CBD [central business district], race, household type and size. A descriptive analysis of maps of these characteristics is followed by simple statistical tests of relations among the variables, in particular distance from the city center. Predictable and strong patterns of spatial structure are consonant with expectations from economic, social, geographic and political urban theory." Data concern King County, Washington, for the period 1980-1985, (the city of Seattle) and are from local sources, including the Puget Sound Council of Governments.

Age Factors↗

Spatial variation in insect community and species responses to habitat loss and plant community composition.

Several experimental studies have examined species responses to manipulations of habitat area and spatial arrangement, but plant composition and spatial variation in species distributions also affect animal responses to habitat alteration. We used an experimental approach to study the combined effects of habitat area, edge, and plant community composition on the spatial structure of insect species richness and composition. The abundance of three guilds (herbivores, predators and parasitoids) and individual species were also analyzed. Habitat patches were created that differed in area and edge by selectively mowing portions of 15 mx15 m plots in a 1.7-ha old field. Spatial and environmental variables were used to predict insect responses in separate multiple regression and ordination models. The variation in species responses due to spatial and environmental variables was then partitioned by combining these variables into an overall regression or ordination. Spatial and environmental variables contributed similar percentages to the total variance in insect species richness, abundance or composition. No significant effects of habitat area were observed in any response variable. Herbivore abundance showed positive responses to legume or grass cover, as well as spatial variation that was unrelated to environmental variables. Predators and parasitoids had greater effects of plant species richness and habitat edge, and less unexplained spatial variation. Individual species differed in their responses to plant variables, depending on host specialization or intraspecific aggregation. Our study highlights the importance of plant community composition and spatial variation apart from environmental variables. Spatial variation stems both from species responses to environmental features as well as species differences in habitat specialization and intraspecific aggregation.

Animals↗

Oscillations by symmetry breaking in homogeneous networks with electrical coupling.

In many biological systems, the electrical coupling of nonoscillating cells generates synchronized membrane potential oscillations. This work describes a dynamical mechanism in which the electrical coupling of identical nonoscillating cells destabilizes the homogeneous fixed point and leads to network oscillations via a Hopf bifurcation. Each cell is described by a passive membrane potential and additional internal variables. The dynamics of the internal variables, in isolation, is oscillatory, but their interaction with the membrane potential damps the oscillations and therefore constructs nonoscillatory cells. The electrical coupling reveals the oscillatory nature of the internal variables and generates network oscillations. This mechanism is analyzed near the bifurcation point, where the spatial structure of the membrane potential oscillations is determined by the network architecture and in the limit of strong coupling, where the membrane potentials of all cells oscillate in-phase and multiple cluster states dominate the dynamics. In particular, we have derived an asymptotic behavior for the spatial fluctuations in the limit of strong coupling in fully connected networks and in a one-dimensional lattice architecture.

Journal Article↗

Sensitivity analyses for ecological regression.

In many ecological regression studies investigating associations between environmental exposures and health outcomes, the observed relative risks are in the range 1.0-2.0. The interpretation of such small relative risks is difficult due to a variety of biases--some of which are unique to ecological data, since they arise from within-area variability in exposures/confounders. The potential for residual spatial dependence, due to unmeasured confounders and/or data anomalies with spatial structure, must also be considered, though it often will be of secondary importance when compared to the likely effects of unmeasured confounding and within-area variability in exposures/confounders. Methods for addressing sensitivity to these issues are described, along with an approach for assessing the implications of spatial dependence. An ecological study of the association between myocardial infarction and magnesium is critically reevaluated to determine potential sources of bias. It is argued that the sophistication of the statistical analysis should not outweigh the quality of the data, and that finessing models for spatial dependence will often not be merited in the context of ecological regression.

Bias↗

Isolation and characterization of the gene encoding the muscle-specific isozyme of human phosphoglycerate mutase.

The human muscle-specific phosphoglycerate mutase encoding gene (PGAM-M) has been cloned from a genomic cosmid library and sequenced. The sequence corresponding to the coding region was evaluated and revised by sequencing of the protein itself, fully confirming our results. The amino acid sequence of the M isozyme presented a 80.6% homology with the B isozyme (non-muscle-specific isozyme), a value higher than previously reported. The PGAM-M gene is composed of three exons, which consist of 454, 180 and 202 bp, respectively, and are separated by two introns of 103 bp and approx. 5.6 kb, respectively. Comparison of the structure of the human PGAM-M gene with that coding for human bisphosphoglycerate mutase, an erythroid-specific enzyme belonging to the same multifunctional enzyme family, revealed that the location of the second intron is similar in each gene and corresponds to a tertiary subdomain in the spatial structure of the protein. The transcription start point (tsp) in the PGAM-M gene was identified by both primer extension and S1 nuclease-protection experiments. A TATA-box-like element was observed 29 bp upstream from the tsp; the sequence ATTGG, inverse/complementary to CCAAT-box, was found 40 bp upstream from the supposed TATA box. No muscle-specific consensus sequences could be detected in the 5'-untranslated region. Only one polyadenylation AATAAA signal was observed in the short 3'-untranslated region (43 bp long). Finally, only one copy of this gene is present in the human genome instead of the several copies found for the PGAM-B gene, suggesting the possible evolutionary origin of the muscle subunit in a modified copy of the PGAM-B gene.

Amino Acid Sequence↗

Identification of homologous core structures.

Using a large database of protein structure-structure alignments, we test a new method for distinguishing homologous and "analogous" structural neighbors. The homologous neighbors included in the test set show no detectable sequence similarity, but they may be well superimposed and show functional similarity or other evidence of evolutionary relationship. Analogous neighbors also show no sequence similarity and may be well superimposed, but they have different functions and their structural similarity may be the result of convergent evolution. Confirming results of other analyses, we find that remote homologs and analogs are not well distinguished by measures of pairwise structural similarity, including the percentage of identical residues and root-mean-square (RMS) superposition residual. We show, however, that with structure-structure alignments of analogous neighbors rarely superimpose the particular substructure that is shared among homologous neighbors. We call this characteristic substructure the homologous core structure (HCS), and we show that a cross-validated test for presence of the HCS correctly identifies 75% of remote homologs with a false-positive rate of 16% analogs, significantly better than discrimination by RMS or other measures of pairwise similarity. The HCS describes conservation of spatial structure within a protein family in much the way that a sequence motif describes sequence conservation. We suggest that it may be used in the same way, to identify homologous neighbors at greater evolutionary distance than is possible by pairwise comparison.

Amino Acid Sequence↗

The posttranslational concept of protein folding: how valid is it?

Two concepts of protein folding are known. One of them, the cotranslational concept, states that a protein folds during the synthesis of the polypeptide chain on the ribosome. According to the other, the posttranslational concept, the protein starts to fold just after the synthesis of its polypeptide chain. This article attempts to show that the posttranslational concept is hardly suited to solve the problem of protein folding. In our opinion, polypeptide chains cannot be represented as random coils. They are stiff chain-like macromolecules rather than flexible ones: the single bond rotational barriers of a polypeptide substantially exceed the accepted standard values; even in strong denaturing conditions, a protein possesses a considerable amount of residual folded structures. We believe that the popular "hierarchical" models for the protein folding mechanism are not realistic because the formation of secondary and tertiary structures of proteins occurs simultaneously and cooperatively. The time for the elongation of a polypeptide chain by one amino acid residue during biosynthesis exceeds considerably the time of the formation of alpha-helices and beta-sheets in proteins as well as the time supposed for the spatial structure formation of a native protein during renaturation. Thus, we believe that the mechanism of protein folding in vivo cannot be clarified by denaturation-renaturation experiments. In our opinion, the phenomenon of protein renaturation is no more than the restoration of native protein conformation (which initially forms cotranslationally) disrupted during denaturation, and thus denaturation-renaturation experiments cannot serve as a model to clarify the mechanism of protein folding.

Models, Chemical↗

Development of spatial and temporal selectivity in the suprasylvian visual cortex of the cat.

We have studied the development of the spatial and temporal properties of neurons in the medial bank of the suprasylvian visual cortex (PMLS) in kittens aged between 9 d and 8 weeks. Quantitative measurements were made of the responses to drifting high-contrast gratings of optimum orientation and direction of motion, but varying in spatial and temporal frequency. The spatial resolution ("acuity") of cells increased rapidly and was fully mature (over 2 cycles/deg for the best cells) at 3 weeks of age. The optimum spatial frequency also tended to improve and reached adult values (around 0.5 cycles/deg for the best cells) at about the end of the third week. In younger kittens, the spatial resolution of neurons was not obviously correlated with the eccentricity of their receptive fields, but in older animals acuity was clearly elevated for receptive fields in the central visual field. The proportion of "low-pass" cells (showing no obvious attenuation of response for gratings of low spatial frequency) decreased with age and simultaneously there was a slight increase in the mean spatial bandwidth of "bandpass" cells. Responses to drifting sinusoidal gratings were generally dominated by an unmodulated elevation of discharge at all ages. In tests with stationary, contrast-modulated gratings presented at different spatial positions, cells in the youngest kittens behaved nonlinearly and showed mainly an unmodulated increase in discharge, whereas in older kittens, as in adult cats, most neurons responded to contrast-modulated gratings with a small, phase-dependent response at the temporal frequency of modulation and a larger component at twice the fundamental frequency. None of the cells recorded at any age had a true "null position." As in adult PMLS, the widths of receptive fields in kittens were, on average, about twice the size of the preferred spatial period (4 times the preferred bar width). At all ages, therefore, neurons in PMLS resembled striate complex cells with respect to the nonlinearity of their responses and the spatial structure of their receptive fields. The preferred temporal frequency and high-temporal-frequency cutoff also improved, on average, during the first 3 weeks of life, and the range of temporal frequencies over which cells responded continued to increase until at least 8 weeks. Although the low-spatial-frequency inhibition that creates spatial bandpass characteristics probably depends on cortical mechanisms, the postnatal development of both temporal and spatial resolution might well be limited by maturation at the level of the retina.

Animals↗

Sociobiology and HLA genetic polymorphism in hill tribes, the Irula of the Nilgiri hills and the Malayali of the Shevroy hills, south India.

Two endogamous tribes of Tamil Nadu, South India, the Irula of the Nilgiri hills and the Malayali of the Shevroy hills, were studied for their sociobiology and HLA polymorphism. For sociobiological studies 166 marriages in the Irula and 368 marriages in the Malayali were recorded. The number and spatial distribution of patrilineal clans and their marriageable range (number of clans from which the brides came) were studied. Eight clans in the Irula and 16 clans in the Malayali were identified. Of these the Kuppar of the Irula and the Malayan of Malayali were the largest clans, and both of them had the greatest marriageable range. The numerical strength and the resultant spatial distribution correlated well with the marriageable range. HLA-A, B, and DR polymorphism was studied on 191 Irula and 42 Malayali following standard procedures. HLA typing revealed high frequencies (> 10%) of alleles HLA-A2, A9, A11, B17, B35, B40, DR2, and DR7 in both tribes, but the Irula had elevated HLA-A10, B8, and DR8 frequencies and the Malayali had elevated HLA-A31, B7, DR4, and DR5 frequencies. Two-locus haplotypes A10-B8 and A2-B5 were identified in both tribes, but A11-B40 and A2-B53 were present only in the Irula and A33-B44 and B15-DR6 were present only in the Malayali. The sociobiology of the Irula was correlated to the HLA genetic profile. The Irula sample was stratified based on clan and HLA data; The Kuppar clan was closer to the Kalkatti, the second largest clan, than to the Pungar and the Sambar clans. Thus the numerical strength and spatial distribution of various exogamous clans, presumably a result of migration during different periods of history, is reflected in the marriageable range and thus in the genetic distance. In studying HLA or any other genetic polymorphism of an endogamous tribe or caste, one needs to consider the social structure, spatial distribution, and marriageable range.

Emigration and Immigration↗

Sustained and transient properties of chromatic and luminance systems.

Reaction times were measured to 450 and 650 mm test increments to examine the temporal behavior of the chromatic and luminance systems. A response-terminated random foreperiod paradigm was employed. Stimuli consisted of chromatic test increments upon backgrounds of varying spatial structure. Conditions were chosen which may preferentially favor the reaction time response being mediated by the chromatic or luminance systems. The temporal properties of the chromatic and luminance systems were demonstrated by the shape of the estimated hazard functions of the reaction time distributions. When the white background was spatially coincident with the test field, the hazard functions showed a relatively small peak. As white sectors were added to the annulus surround (introducing spatial transients between test and background fields), however, the hazard functions became more and more peaked. The hazard functions of the luminance system were estimated by assuming that the chromatic and luminance systems function in parallel. We concluded from the results that the chromatic system may be characterized as a quasi-sustained mechanism and the luminance system as a transient mechanism.

Color Perception↗