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Topographic shear and the relation of ocular dominance columns to orientation columns in primate and cat visual cortex.

Shear has been known to exist for many years in the topographic structure of the primary visual cortex, but has received little attention in the modeling literature. Although the topographic map of V1 is largely conformal (i.e. zero shear), several groups have observed topographic shear in the region of the V1/V2 border. Furthermore, shear has also been revealed by anisotropy of cortical magnification factor within a single ocular dominance column. In the present paper, we make a functional hypothesis: the major axis of the topographic shear tensor provides cortical neurons with a preferred direction of orientation tuning. We demonstrate that isotropic neuronal summation of a sheared topographic map, in the presence of additional random shear, can provide the major features of cortical functional architecture with the ocular dominance column system acting as the principal source of the shear tensor. The major principal axis of the shear tensor determines the direction and its eigenvalues the relative strength of cortical orientation preference. This hypothesis is then shown to be qualitatively consistent with a variety of experimental results on cat and monkey orientation column properties obtained from optical recording and from other anatomical and physiological techniques. In addition, we show that a recent result of Das and Gilbert (Das, A., & Gilbert, C. D., 1997. Distortions of visuotopic map match orientation singularities in primary visual cortex. Nature, 387, 594-598) is consistent with an infinite set of parameterized solutions for the cortical map. We exploit this freedom to choose a particular instance of the Das-Gilbert solution set which is consistent with the full range of local spatial structure in V1. These results suggest that further relationships between ocular dominance columns, orientation columns, and local topography may be revealed by experimental testing.

Journal Article↗

Cortactin tyrosine phosphorylation requires Rac1 activity and association with the cortical actin cytoskeleton.

Cortactin is an F-actin binding protein that activates actin-related protein 2/3 complex and is localized within lamellipodia. Cortactin is a substrate for Src and other protein tyrosine kinases involved in cell motility, where its phosphorylation on tyrosines 421, 466, and 482 in the carboxy terminus is required for cell movement and metastasis. In spite of the importance of cortactin tyrosine phosphorylation in cell motility, little is known regarding the structural, spatial, or signaling requirements regulating cortactin tyrosine phosphorylation. Herein, we report that phosphorylation of cortactin tyrosine residues in the carboxy terminus requires the aminoterminal domain and Rac1-mediated localization to the cell periphery. Phosphorylation-specific antibodies directed against tyrosine 421 and 466 were produced to study the regulation and localization of tyrosine phosphorylated cortactin. Phosphorylation of cortactin tyrosine 421 and 466 was elevated in response to Src, epidermal growth factor receptor and Rac1 activation, and tyrosine 421 phosphorylated cortactin localized with F-actin in lamellipodia and podosomes. Cortactin tyrosine phosphorylation is progressive, with tyrosine 421 phosphorylation required for phosphorylation of tyrosine 466. These results indicate that cortactin tyrosine phosphorylation requires Rac1-induced cortactin targeting to cortical actin networks, where it is tyrosine phosphorylated in hierarchical manner that is closely coordinated with its ability to regulate actin dynamics.

Actins↗

Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking.

A major problem in genome annotation is whether it is valid to transfer the function from a characterised protein to a homologue of unknown activity. Here, we show that one can employ a strategy that uses a structure-based prediction of protein functional sites to assess the reliability of functional inheritance. We have automated and benchmarked a method based on the evolutionary trace approach. Using a multiple sequence alignment, we identified invariant polar residues, which were then mapped onto the protein structure. Spatial clusters of these invariant residues formed the predicted functional site. For 68 of 86 proteins examined, the method yielded information about the observed functional site. This algorithm for functional site prediction was then used to assess the validity of transferring the function between homologues. This procedure was tested on 18 pairs of homologous proteins with unrelated function and 70 pairs of proteins with related function, and was shown to be 94 % accurate. This automated method could be linked to schemes for genome annotation. Finally, we examined the use of functional site prediction in protein-protein and protein-DNA docking. The use of predicted functional sites was shown to filter putative docked complexes with a discrimination similar to that obtained by manually including biological information about active sites or DNA-binding residues.

Algorithms↗

An analysis of selection on a colour polymorphism in the northern leopard frog.

In this study, we investigated the role of selection in the maintenance of a dorsal colour polymorphism in natural populations of the northern leopard frog, Rana pipiens. We determined genetic structure both spatially and temporally from a suite of putatively neutral molecular markers and tested whether or not the colour locus exhibited patterns of genetic variation that differed from those of the neutral loci. Spatial genetic structure at the colour locus was indistinguishable from structure at neutral loci [95% confidence intervals of F(ST) (neutral) = (0.07, 0.35), F(ST) (colour locus) = 0.114]. In the temporal analysis, we found that the variance among populations in the change in allele frequency at the colour locus (equal to 0.004) lies within the 95% confidence intervals for the variance among populations in changes in allele frequencies at neutral loci. In light of our inability to show evidence for the selective maintenance of the colour polymorphism, we used computer simulations to infer the power of our spatial and temporal techniques to detect selection. The computer simulations showed that although the strength of selection (s) would need to be relatively strong to have been detected by the temporal approach (s = 0.1-0.4, depending on the model tested), the spatial analysis would have detected all but weak selection (s = 0.01-0.04, depending on the model tested). This study illustrates the importance of using a locus comparison approach to detect evidence for selective maintenance before conducting studies to measure the selective mechanisms maintaining a polymorphism.

Alleles↗

Synthesis, conformational studies, and investigations on the estrogen receptor binding of [R/S-1-(2,6-dichloro-4-hydroxyphenyl)ethylenediamine]platinum(II) complexes.

The syntheses, conformational studies, and investigations on the estrogen receptor binding of [R/S-1-(2,6-dichloro-4-hydroxyphenyl)ethylenediamine]platinum(II) complexes (1-PtL2, 2L = leaving groups) are described. A Strecker synthesis using the 2,6-dichloro-4-methoxybenzaldehyde, NaCN, and NH4Cl afforded the cyanoamine 1b, which was subsequently reduced with LiAlH4 to give the R/S-1-(2,6-dichloro-4-methoxyphenyl)ethylenediamine 1a. Ether cleavage with BBr3 yielded R/S-1-(2,6-dichloro-4-hydroxyphenyl)ethylenediamine 1 which was coordinated to platinum(II) by use of K2PtCl4 (1-PtCl2) and K2PtI4 (1-PtI2), respectively. Reaction of 1-PtI2 with Ag2SO4 and coordination of tartronic acid led to the [R/S-1-(2,6-dichloro-4- hydroxyphenyl)ethylenediamine][hydroxymalonato]platinum(II) complex (1-Pt(MalOH)). The spatial structure of 1 and its complexes was evaluated by spectroscopic and molecular modeling methods. In solution the complexes adopt a structure very similar to estradiol. However, the in vitro and in vivo tests for the compounds indicated neither affinity to the estrogen receptor nor estrogenic properties.

Cell Line↗

Bioluminescence in oceanology.

For analytical purposes bioluminescence can be used in three main ways: 1. luminescence measurement of bioluminescent system components isolated in vitro; 2. determination of luminous organisms' reaction to the in vivo test-action; 3. measurement of bioluminescence in marine ecological systems. The majority of the reports of this Symposium are dealing with the first two topics. The aim of our presentation is to draw attention to the third one. The possibilities of bioluminescent analysis are wider than its traditional scheme of applications in the laboratory, when the emitting system is withdrawn from a native source and is placed in a cuvette of the light measuring device. The reverse scheme is also possible, i.e. the device can be introduced into light emitting system such as a marine biocenosis--the community of the sea inhabitants--where we obtain a highly sensitive and rapid means of gaining the information on the vital activity of marine ecosystems, i.e. their spatial structure, rhythms, man's influence upon them, etc. The present communication will consider the possibilities of this form of bioluminescent analysis.

Circadian Rhythm↗

(S)-2-chloro-2-fluoroethanoyl isocyanate, a chiral derivative of trichloroacetyl isocyanate.

Carbamate diastereomers 3b-18b were prepared from easily accessible (S)-2-chloro-2-fluoroethanoyl isocyanate (1) and various secondary chiral alcohols. Compound 1 as a chiral analog of trichloroacetyl isocyanate undergoes the reaction with alcohols very fast, thus blocking the hydroxyl group for the purposes of NMR investigation. Moreover, the correlation of stereochemistry of 3b-18b with their (1)H NMR spectra revealed that the constitution as well as configuration influences regularly the values of chemical shift difference (deltadelta = delta(R) - delta(S)) except for those diastereomers bearing simple alkyl groups in the molecule. Spectral as well as crystallographic data manifest the predominant planar conformation of the central part of the molecule. Due to the good accessibility and high reactivity in particular, the acylisocyanate 1 might be considered, to some extent, an alternative for TAI giving additional information on a compound's spatial structure.

Journal Article↗

Microsolvation of an ionic dopant in small (4)He clusters: OH(+)((3)sigma)((4)He)(N) via genetic algorithm optimizations.

The optimized spatial structures of the small clusters (with N up to 33) formed by an increasing number of (4)He atoms, which act as a microsolvent surrounding the OH(+) ionic molecular dopant, are obtained using a sum-of-potentials scheme corrected by three-body (3B) effects. The most stable structures are generated using the type of genetic algorithm described herein, and the sequential formation of regular shell structures is analyzed in detail. Possible quantum corrections for both the solvent distributions and the stable energetics are analyzed and discussed.

Journal Article↗

Adenosine triphosphatase activities in plasma liver membranes of rats treated with DDT and toxaphene.

The effect of exposure to chlorinated insecticides (DDT and toxaphene) on Na+,K+-ATPase, Mg2+-ATPase and Ca2+-ATPase activities of the plasma membrane of hepatocytes was determined. Acute treatment with DDT (200 mg per kg body weight) or toxaphene (110 mg per kg body weight) produced a significant decrease in Na+,K+-ATPase activity (80% and 85%, respectively) 24 h after treatment. DDT also produced a 30% decrease in Mg2+-ATPase and Ca2+-ATPase activity, but toxaphene treatment did not modify these enzymes. The effect of exposure to daily doses of DDT (30 mg per kg body weight) or toxaphene (16.5 mg per kg body weight) for a period of 3.5 months was also studied. Animals were sacrificed at 15-day intervals and results showed that Na+,K+-ATPase activity decreased 80% from the beginning of each treatment and the activity remained low throughout the treatment period. DDT, but not toxaphene, also led to a decrease in Mg2+-ATPase (20%) and Ca2+-ATPase (35%) activity. The low values observed from the beginning remained low throughout the treatment period. We believe that the general mechanism of ATPase inhibition by organochloride compounds could be the result of its interaction with membrane lipid components, although some differences could arise from differences in their spatial structure.

Adenosine Triphosphatases↗

Localized basis orbitals: minimization of 2-electron integrals array and orthonormality of basis set.

A new scheme for deriving localized basis orbitals (LBOs) and for obtaining integral transformations from the basis orbitals (BOs) to the LBOs has been introduced. The scheme was tested at the ab initio Hartree-Fock level using the STO-3G basis set. It has been revealed that it provides results that are close to the conventional ab initio approximations for various physical-chemical properties. At the same time, both the number of differential overlaps and the number of electron repulsion integrals (ERIs) grow with the system size notably slower than those calculated for the usual BOs. The power exponent for ERI/LBO is typically smaller by 0.3-0.6 than that for ERI/BO. The exponent reaches the value of 1.69 even for triglycine (24 atoms only), which represents a relatively small molecular model. Thus, the localization of the BOs (using LBOs) may result in additional improvements in efficiency even for electronically delocalized systems. It was shown that ERI/LBO is particularly efficient for systems with complex spatial structures (including conjugated species). The obtained results indicate that the proposed scheme could be included in computational methods targeted at calculating large molecular systems (which achieve linear scaling for more distant interactions). Neglecting ERI/LBO does not depend on the delocalization of the localized MO using ERI/LBO. The orthogonality and locality of the LBOs should make them useful in methods based on dividing the system into orthogonal subsystems.

Journal Article↗

Optimizing UV laser focus profiles for improved MALDI performance.

Matrix assisted laser desorption/ionization (MALDI) applications, such as proteomics, genomics, clinical profiling and MALDI imaging, have created a growing demand for faster instrumentation. Since the commonly used nitrogen lasers have throughput and life span limitations, diode-pumped solid-state lasers are an alternative. Unfortunately this type of laser shows clear performance limitations in MALDI in terms of sensitivity, resolution and ease of use, for applications such as thin-layer sample preparations, acceptance of various matrices (e.g. DHB for glycopeptides) and MALDI imaging. While it is obvious that the MALDI process has some dependence on the characteristics of the laser used, it is unclear which features are the most critical in determining laser performance for MALDI. In this paper we show, for the first time, that a spatially structured laser beam profile in lieu of a Gaussian profile is of striking importance. This result enabled us to design diode-pumped Nd : YAG lasers that on various critical applications perform as well for MALDI as the nitrogen lasers and in some respects even better. The modulation of the beam profile appears to be a new parameter for optimizing the MALDI process. In addition, the results trigger new questions directing us to a better understanding of the MALDI process.

Algorithms↗

Nd:YAG laser irradiation of an eye model: experimental analysis.

This work reviews a series of experiments performed on an eye model to study physical effect relevant for a safe and effective use of the Q-switched Nd:YAG laser in ophthalmic microsurgery. The breakdown probability per laser pulse has been found to depend exponentially on the reciprocal laser field. This indicates that, as in transparent solids, electron avalanche ionization is likely the main mechanism for optical breakdown in liquids. Shielding of the retina, by the laser-induced plasma, is not very effective, but an appreciable degree of shielding is present, in burst operation, even after membrane disruption. A backscattered beam, which presents the typical properties of stimulated Brillouin scattering, has been observed in the eye model, with a threshold of approximately 5 X 10(9) W/cm2. This beam, which presents an irregular spatial structure with peaks of irradiance well above the average value, may produce damage of the internal wall of the cornea.

Eye↗

Determinants of proton relaxation rates in tissue.

It is well established that the longitudinal magnetic relaxation rate of solvent water protons, 1/T1, increases markedly in homogeneous protein solutions as the magnetic field is reduced well below the traditional NMR range. For a 5% solution of protein of 10(5) Da, for example, 1/T1 increases from about 50% above the pure water rate of 20 MHz to five times the water rate at 0.01 MHz. For tissue, including blood, the behavior is similar. Data for blood show that extracellular water has ready access to the hemoglobin inside red blood cells, which causes the enhanced relaxation. The extent to which cell water can sample the spatial structure of soft tissue, and how this structure influences relaxation rates, is as yet unknown. Nonetheless, the relaxation data for tissue can be accommodated within the conceptual framework developed earlier for analyzing homogeneous solutions of diamagnetic proteins. The variation of 1/T1 with field differs among tissues, and its magnitude at a given field can vary by more than a factor of three, far more than does the water content of the tissues. Solute complexes of paramagnetic ions with macromolecules, which increase the relaxation rates of solvent protons, can be introduced intravenously in tissue. They are known to accumulate in specific organs, and therefore have potential utility as contrast-enhancing agents in NMR imaging. Mn2+ and Gd3+, for example, produce characteristic dependences of 1/T1 on magnetic field that vary with the chemical state of the agent. The possibility exists, therefore, for monitoring the in vivo biochemistry of these agents.

Animals↗

Opposite behavior of two isozymes when refolding in the presence of non-ionic detergents.

GroEL has a greater affinity for the mitochondrial isozyme (mAAT) of aspartate aminotransferase than for its cytosolic counterpart (cAAT) (Mattingly JR Jr, Iriarte A, Martinez-Carrion M, 1995, J Biol Chem 270:1138-1148), two proteins that share a high degree of sequence similarity and an almost identical spatial structure. The effect of detergents on the refolding of these large, dimeric isozymes parallels this difference in behavior. The presence of non-ionic detergents such as Triton X-100 or lubrol at concentrations above their critical micelle concentration (CMC) interferes with reactivation of mAAT unfolded in guanidinium chloride but increases the yield of cAAT refolding at low temperatures. The inhibitory effect of detergents on the reactivation of mAAT decreases progressively as the addition of detergents is delayed after starting the refolding reaction. The rate of disappearance of the species with affinity for binding detergents coincides with the slowest of the two rate-limiting steps detected in the refolding pathway of mAAT. Limited proteolysis studies indicate that the overall structure of the detergent-bound mAAT resembles that of the protein in a complex with GroEL. The mAAT folding intermediates trapped in the presence of detergents can resume reactivation either upon dilution of the detergent below its CMC or by adding beta-cyclodextrin. Thus, isolation of otherwise transient productive folding intermediates for further characterization is possible through the use of detergents.

Anilino Naphthalenesulfonates↗

A hierarchical model for spatially clustered disease rates.

Maps of regional disease rates are potentially useful tools in examining spatial patterns of disease and for identifying clusters. Bayes and empirical Bayes approaches to this problem have proven useful in smoothing crude maps of disease rates. In recent years, models including both spatially correlated random effects and spatially unstructured random effects have been very popular. The spatially correlated random effects have been proposed in an attempt to capture a general clustering in the data. As an alternative, we propose replacing the spatially structured random effect with fixed clustering effects associated with particular areas. A reversible jump Markov chain Monte Carlo (RJMCMC) algorithm for posterior inference is described. We illustrate the model using the well-known New York leukaemia data.

Cluster Analysis↗

A method for testing the significance of geographical correlations with application to industrial lung cancer in France.

This paper discusses some of the problems encountered when testing significance in geographical epidemiology where variables typically exhibit some spatial autocorrelation. A test of partial correlation between spatially autocorrelated variables is presented. It is based on evaluation of an effective sample size which takes account of spatial structure. Performance is assessed by Monte Carlo simulation. The proposed method is used to study male lung cancer rates in specific industries in France.

France↗

Synthetic cancer variables and the construction and testing of synthetic risk maps.

Cancer cluster investigations are usually univariate in nature; they focus on a particular cancer, such as leukaemia, and attempt to determine whether excess risk is associated with a suspected cancer-causing agent. Although several causes of death (such as leukaemia, lymphoma, Hodgkin's) may be considered, the approach is univariate because the causes of death are analysed sequentially and independently of one another. This approach is consistent with a one-cause one-effect model. Rarely, however, is the action of a carcinogen manifested at only one body site, and correlations among causes of death are the norm rather than the exception. A multiple effects model is therefore appropriate, and the multivariate nature of cancer mortality data should be exploited when exploring geographic pattern in cancer risks. This paper describes such an approach. We construct maps based on a principal components analysis of cancer mortality rates from different geographic areas. The resulting principal components are called synthetic cancer variables (SCVs), and maps of the SCV scores are synthetic risk maps (SRMs). These maps quantify geographic variation in cancer risk at several body sites simultaneously, and may be analysed for (1) spatial structure and (2) geographic association with potential risk factors. As an example, we use synthetic risk maps to determine whether high-risk counties in Illinois cluster near nuclear facilities. Much work remains to be done, but synthetic cancer risk maps appear to be a useful tool for quantifying geographic pattern and multivariate structure in cancer mortality.

Air Pollutants, Radioactive↗

cDNA-directed expression of two allelic variants of cytochrome P450 2C11 using COS1 and SF21 insect cells.

Cytochromes P450 (CYP) are ubiquitous enzymes which metabolize multiple endogenous and exogenous substrates. CYP2C11 is the most abundant among the P450s present in untreated rat liver (approximately 50% of total P450) and is known for metabolizing testosterone mainly in positions 2 alpha and 16 alpha. In Gunn rats, the specific enzymatic activities of CYP2C11 are decreased by 90%, although the protein is present at levels similar to that of the Wistar reference strain. In order to explain this difference, we cloned and expressed CYP2C11 Wistar and Gunn cDNAs in two heterologous systems. Three mutations were identified in Gunn CYP2C11 form: Val4 --> Ala in the transmembrane region, Asn116 --> Ser in the substrate recognition site SRS-1, and Phe187 --> Leu in the (E --> F) interhelical region when compared to the spatial structure of CYP101. Sf21 insect cells displayed high yields of expressed CYP2C11 proteins (up to 2 nmol CYP2C11/mg microsomal proteins) which are more than 60-fold those observed in COS1 cells and 4-fold those present in hepatic microsomes. Testosterone-hydroxylating activities from CYP2C11 Gunn expressed in insect cells were decreased by 40% when compared to CYP2C11 Wistar, reflecting with a lesser extent the decrease we have previously reported in liver microsomes. The high level of active protein obtained with the baculovirus/insect cell expression system will be useful to analyze activities of site-directed mutants of CYP2C11 in order to elucidate the respective influence of the identified mutations on the enzymatic activities.

Alleles↗