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PubMed2006

Unique features of TRIM5alpha among closely related human TRIM family members.

The tripartite motif (TRIM) protein, TRIM5alpha, restricts some retroviruses, including human immunodeficiency virus (HIV-1), from infecting the cells of particular species. TRIM proteins contain RING, B-box, coiled-coil and, in some cases, B30.2(SPRY) domains. We investigated the properties of human TRIM family members closely related to TRIM5. These TRIM proteins, like TRIM5alpha, assembled into homotrimers and co-localized in the cytoplasm with TRIM5alpha. TRIM5alpha turned over more rapidly than related TRIM proteins. TRIM5alpha, TRIM34 and TRIM6 associated with HIV-1 capsid-nucleocapsid complexes assembled in vitro; the TRIM5alpha and TRIM34 interactions with these complexes were dependent on their B30.2(SPRY) domains. Only TRIM5alpha potently restricted infection by the retroviruses studied; overexpression of TRIM34 resulted in modest inhibition of simian immunodeficiency virus (SIV(mac)) infection. In contrast to the other TRIM genes examined, TRIM5 exhibited evidence of positive selection. The unique features of TRIM5alpha among its TRIM relatives underscore its special status as an antiviral factor.

Adaptor Proteins, Signal Transducing↗
PubMed1995

Pagetoid melanocytosis. Histologic features in benign and malignant lesions.

Pagetoid melanocytosis (PM), the upward discontinuous extension of melanocytes into the superficial epidermis, although generally considered a histologic feature of malignancy, may be seen in certain benign melanocytic lesions. To formulate the histologic criteria for distinction between benign and malignant PM, we examined 218 melanocytic tumors, including melanomas, Spitz nevi, nevi of palms and soles, pigmented spindle cell nevi, recurrent nevi, vulvar nevi, nevi of infancy and early childhood, and ordinary acquired nevi. We found PM to be present in 96% of melanomas, 38% of Spitz nevi, 61% of nevi of palms and soles, 20% of pigmented spindle cell nevi, 60% of recurrent nevi, 80% of vulvar nevi, and none of the ordinary acquired nevi. All the nevi of infancy and early childhood showed PM, but they had been selected for that feature. In melanomas, PM showed significant cellular atypia (81%), which was extensive and diffuse, and in 13% it extended laterally beyond the underlying junctional component. In the benign lesions, cellular atypia was generally absent, nor was lateral extension present, and PM was usually focal or multifocal rather than diffuse and not extensive. Although PM should be considered a tocsin for malignant melanoma, it may also occur in certain benign melanocytic lesions. Accurate interpretation depends on evaluation of all of the pertinent histologic and clinical findings.

Adolescent↗
PubMed2005

Triggered release of proteins from emulsan-alginate beads.

Emulsan/alginate beads were studied for protein adsorption and stability in the context of controlled release. The beads, 400 +/- 80 microm diameter with approximately 10% emulsan content, offer unusual opportunities for delivery of proteins due to the natural ability of emulsan to bind proteins, coupled with the selective biological activation features of this complex lipoheteropolysaccharide. The binding capacity of azo-bovine serum albumin by the emulsan/alginate beads was 0.637 +/- 0.004 vs. 0.170 +/- 0.007 microg/mg for beads formed from alginate alone. In additional protein adsorption experiments, the lipase and subtilisin maintained activity when adsorbed to the emulsan/alginate beads albeit with lower specific activity when compared to the enzyme free in solution. However, the half life of the adsorbed enzyme was significantly higher than the free forms. To explore functional utility of this system, two types of triggered release were studied in the context of these bead systems. First, azo-BSA as a model protein was physically bound to emulsan/alginate beads and then selectively released by triggering with subtilisin, a serine protease, which cleaves the azo dye, sulfanilic acid, from the bound protein. In absence of subtilisin no triggered release was observed. Second, azo-BSA as a prodrug model, was adsorbed to the emulsan/alginate beads and then release of the dye was demonstrated by lipase treatment which cleaves the fatty acid esters from the emulsan structure to release the bound protein. The results establish the versatility and utility of emulsan-based beads for protein binding and triggered release.

Acinetobacter↗
PubMed1999

Texture filling-in and texture segregation revealed by transient masking.

When a texture pattern was briefly presented followed by a small annular mask, it was found that the central area of the texture was strongly suppressed within the mask. Analogous to filling-in of brightness in a uniform luminance area (Paradiso, M. A. & Nakayama, K. (1991) Vision Research, 31, 1221-1236), this phenomenon demonstrates filling-in of texture; the texture area was unperceived because filling-in of the texture area was interrupted by the contour in the mask. However, odd local features within the texture, which were assumed to pop out, were selectively perceived while other features were suppressed within the mask. These results suggest that: (1) rapid pattern segregation occurs before and/or separately from texture filling-in, and that (2) filling-in is initiated at boundaries between surfaces rather than at luminance gradients.

Form Perception↗
PubMedDate not supplied

Toward an optimal procedure for variable selection and QSAR model building.

In this work, we report the development of a novel QSAR technique combining genetic algorithms and neural networks for selecting a subset of relevant descriptors and building the optimal neural network architecture for QSAR studies. This technique uses a neural network to map the dependent property of interest with the descriptors preselected by the genetic algorithm. This technique differs from other variable selection techniques combining genetic algorithms to neural networks by two main features: (1) The variable selection search performed by the genetic algorithm is not constrained to a defined number of descriptors. (2) The optimal neural network architecture is explored in parallel with the variable selection by dynamically modifying the size of the hidden layer. By using both artificial data and real biological data, we show that this technique can be used to build both classification and regression models and outperforms simpler variable selection techniques mainly for nonlinear data sets. The results obtained on real data are compared to previous work using other modeling techniques. We also discuss some important issues in building QSAR models and good practices for QSAR studies.

Algorithms↗
PubMed2004

The contribution of spike threshold to the dichotomy of cortical simple and complex cells.

The existence of two classes of cells, simple and complex, discovered by Hubel and Wiesel in 1962, is one of the fundamental features of cat primary visual cortex. A quantitative measure used to distinguish simple and complex cells is the ratio between modulated and unmodulated components of spike responses to drifting gratings, an index that forms a bimodal distribution. We have found that the modulation ratio, when derived from the subthreshold membrane potential instead of from spike rate, is unimodally distributed, but highly skewed. The distribution of the modulation ratio as derived from spike rate can, in turn, be predicted quantitatively by the nonlinear properties of spike threshold applied to the skewed distribution of the subthreshold modulation ratio. Threshold also increases the spatial segregation of ON and OFF regions of the receptive field, a defining attribute of simple cells. The distinction between simple and complex cells is therefore enhanced by threshold, much like the selectivity for stimulus features such as orientation and direction. In this case, however, a continuous distribution in the spatial organization of synaptic inputs is transformed into two distinct classes of cells.

Action Potentials↗
PubMed2002

Diagnostic features of Alzheimer's disease extracted from PET sinograms.

Texture analysis of positron emission tomography (PET) images of the brain is a very difficult task, due to the poor signal to noise ratio. As a consequence, very few techniques can be implemented successfully. We use a new global analysis technique known as the Trace transform triple features. This technique can be applied directly to the raw sinograms to distinguish patients with Alzheimer's disease (AD) from normal volunteers. FDG-PET images of 18 AD and 10 normal controls obtained from the same CTI ECAT-953 scanner were used in this study. The Trace transform triple feature technique was used to extract features that were invariant to scaling, translation and rotation, referred to as invariant features, as well as features that were sensitive to rotation but invariant to scaling and translation, referred to as sensitive features in this study. The features were used to classify the groups using discriminant function analysis. Cross-validation tests using stepwise discriminant function analysis showed that combining both sensitive and invariant features produced the best results, when compared with the clinical diagnosis. Selecting the five best features produces an overall accuracy of 93% with sensitivity of 94% and specificity of 90%. This is comparable with the classification accuracy achieved by Kippenhan et al (1992), using regional metabolic activity.

Adult↗
PubMed2000

An unusual form of purifying selection in a sperm protein.

Protamines are small, highly basic DNA-binding proteins found in the sperm of animals. Interestingly, the proportion of arginine residues in one type of protamine, protamine P1, is about 50% in mammals. Upon closer examination, it was found that both the total number of amino acids and the positions of arginine residues have changed considerably during the course of mammalian evolution. This evolutionary pattern suggests that protamine P1 is under an unusual form of purifying selection, in which the high proportion of arginine residues is maintained but the positions may vary. In this case, we would expect that the rate of nonsynonymous substitution is not particularly low compared with that of synonymous substitution, despite purifying selection. We would also expect that the selection for a high arginine content results in a high frequency of the nucleotide G in the coding region of this gene, because all six arginine codons contain at least one G. These expectations were confirmed in our study of mammalian protamine genes. Analysis of nonmammalian vertebrate genes also showed essentially the same patterns of evolutionary changes, suggesting that this unusual form of purifying selection has been active since the origin of bony vertebrates. The protamine gene of an insect species shows similar patterns, although its purifying selection is less intense. These observations suggest that arginine-rich selection is a general feature of protamine evolution. The driving force for arginine-rich selection appears to be the DNA-binding function of protamine P1 and an interaction with a protein kinase in the fertilized egg.

Amino Acid Sequence↗
PubMed1994

Genetic analysis of 29 kindreds with generalized and pituitary resistance to thyroid hormone. Identification of thirteen novel mutations in the thyroid hormone receptor beta gene.

Resistance to thyroid hormone (RTH), with elevated serum free thyroid hormones and nonsuppressed thyrotropin levels, is either relatively asymptomatic, suggesting a generalized disorder (GRTH) or associated with thyrotoxic features, indicating possible selective pituitary resistance (PRTH). 20 GRTH and 9 PRTH cases, sporadic or dominantly inherited, were analyzed. Affected individuals were heterozygous for single nucleotide substitutions in the thyroid hormone receptor beta gene, except for a single case of a seven nucleotide insertion. With one exception, the corresponding 13 novel and 7 known codon changes localized to and extended the boundaries of two mutation clusters in the hormone-binding domain of the receptor. 15 kindreds shared 6 different mutations, and haplotype analyses of the mutant allele showed that they occurred independently. The majority (14 out of 19) of the recurrent but a minority (1 out of 10) of unique mutations were transitions of CpG dinucleotides. Mutant receptor binding to ligand was moderately or severely impaired and did not correlate with the magnitude of thyroid dysfunction. There was no association between clinical features and the nature or location of a receptor mutation. These observations suggest that GRTH and PRTH are phenotypic variants of the same genetic disorder, whose clinical expression may be modulated by other non-mutation-related factors.

Adolescent↗
PubMed1998

Does competition by health maintenance organizations affect the adoption of cost-containment measures by fee-for-service plans?

How groups insured by fee-for-service health plans react to increased competition from health maintenance organizations (HMOs) is an unresolved question. We investigated whether groups insured by indemnity plans respond to HMO market competition by changing selected health insurance features, such as deductible amounts, stop loss levels, and coinsurance rates, or by adopting utilization management or preferred provider organization (PPO) benefit options. We collected benefit design data for the years 1985 through 1992 from 95 insured groups in 62 US metropolitan statistical areas. Multivariate hazard analysis showed that groups located in markets with higher rates of change in HMO enrollment were less likely to increase deductibles or stop loss levels. Groups located in markets with higher HMO enrollment were more likely to adopt utilization management or PPO benefit options. A group located in a market with an HMO penetration rate of 20% was 65% more likely to have included a PPO option as part of its insurance benefit plan than a group located in a market with an HMO penetration rate of 15% (p < 0.05). Concern about possible adverse selection effects may deter some fee-for-service groups from changing their health insurance coverage. Under some conditions, however, groups insured under fee-for-service plans do respond to managed care competition by changing their insurance benefits to achieve greater cost containment.

Cost Control↗
PubMed2000

Aspects of the failed back syndrome: role of litigation.

OBJECTIVE: A review that attempts to identify the mechanism and causation of persistent or recurring low back pain. DESIGN: A personal assessment of clinical features with a selective review of the literature. RESULTS: Thirty to forty per cent of our population aged 10-65 years report that back trouble occurs on a monthly basis and in 1% to 8% this interferes with work. A definite patho-anatomical cause for the pain is demonstrable in only a minority. It can be deduced that psychosocial factors, including insurance benefits are of importance for this variation. CONCLUSIONS: Neither non-operative nor surgical procedures have a major impact on the capacity for work in this substantial minority of backache sufferers. The main risk factors identified are: Wrong diagnosis, repeated medical certificates for sickness benefits, failed surgery, symptoms incongruous with signs or imaging, multiple spinal procedures, poor social support and poor motivation, psychological illness, clinical depression before or after injury or operation. Pending compensation and delays in settlement are important additional features in claimants for compensation. For patients with unproven diagnostic labels such as 'pain-behaviour', no evidence exists that any type of surgery is cost effective.

Humans↗
PubMed2003

Phosphatidylinositol-3,5-Bisphosphate is a potent and selective inhibitor of acid sphingomyelinase.

Acid sphingomyelinase (A-SMase, EC 3.1.4.12) catalyzes the lysosomal degradation of sphingomyelin to phosphorylcholine and ceramide. Inherited deficiencies of acid sphingomyelinase activity result in various clinical forms of Niemann-Pick disease, which are characterised by massive lysosomal accumulation of sphingomyelin. Sphingomyelin hydrolysis by both, acid sphingomyelinase and membrane-associated neutral sphingomyelinase, plays also an important role in cellular signaling systems regulating proliferation, apoptosis and differentiation. Here, we present a potent and selective novel inhibitor of A-SMase, L-alpha-phosphatidyl-D-myo-inositol-3,5-bisphosphate (PtdIns3,5P2), a naturally occurring substance detected in mammalian, plant and yeast cells. The inhibition constant Ki for the new A-SMase inhibitor PtdIns3,5P2 is 0.53 microM as determined in a micellar assay system with radiolabeled sphingomyelin as substrate and recombinant human A-SMase purified from insect cells. Even at concentrations of up to 50 microM, PtdIns3,5P2 neither decreased plasma membrane-associated, magnesium-dependent neutral sphingomyelinase activity, nor was it an inhibitor of the lysosomal hydrolases beta-hexosaminidase A and acid ceramidase. Other phosphoinositides tested had no or a much weaker effect on acid sphingomyelinase. Different inositol-bisphosphates were studied to elucidate structure-activity relationships for A-SMase inhibition. Our investigations provide an insight into the structural features required for selective, efficient inhibition of acid sphingomyelinase and may also be used as starting point for the development of new potent A-SMase inhibitors optimised for diverse applications.

Dose-Response Relationship, Drug↗
PubMed2006

High resolution photofragment translational spectroscopy studies of the near ultraviolet photolysis of imidazole.

The fragmentation dynamics of imidazole molecules following excitation at 193.3 nm and at many wavelengths in the range of 210< or =lambda(phot)< or =240 nm have been investigated by H Rydberg atom photofragment translational spectroscopy. Long wavelength excitation within this range results in population of the 1 (1)A(")((1)pisigma(*)) excited state, but the 2 (1)A(')<--X (1)A(')(pi(*)<--pi) transition becomes the dominant absorption once lambda(phot)< or =220 nm. The measured energy disposals show parallels with those found in recent studies of the UV photolysis of pyrrole [Cronin et al., Phys Chem. Chem. Phys. 6, 5031 (2004)]. The total kinetic energy release (TKER) spectra display a "fast" feature, centred at TKER approximately 9200 cm(-1). The analysis of the structure evident in the fast feature reveals the selective population of specific in-plane stretching vibrational levels of the imidazolyl cofragment; these fragments are deduced to carry only modest amounts of rotational excitation. Comparison with calculated normal mode vibrational frequencies allows the assignment of the populated levels and a precise determination of the N-H bond strength in imidazole: D(0)=33,240+/-40 cm(-1). The observed energy disposal can be rationalized using Franck-Condon arguments, assuming that the potential energy surface (PES) for the 1 (1)A(")((1)pisigma(*)) state has a topology similar to that of the corresponding (1)pisigma(*) state of pyrrole. As in pyrrole, photoexcitation populates skeletal motions in the S(1) state (in-plane motions in the present case) that are only weakly coupled to the N-H dissociation coordinate and thus map through into the corresponding product vibrations. A second, "slow" feature is increasingly evident in TKER spectra recorded at shorter lambda(phot). This component, which exhibits no recoil anisotropy, is attributed to H atoms formed by the "statistical" decay of highly vibrationally excited ground state molecules. The form of the TKER spectra observed at short lambda(phot) is rationalized by assuming two possible decay routes for imidazole molecules excited to the 2 (1)A(')((1)pipi(*)) state. One involves fast 2 (1)A(')((1)pipi(*)) right arrow-wavy 1 (1)A(")((1)pisigma(*)) radiationless transfer and subsequent fragmentation on the 1 (1)A(')((1)pisigma(*)) PES, yielding fast H atoms (and imidazolyl cofragments)-reminiscent of behavior seen at longer excitation wavelengths where the 1 (1)A(")((1)pisigma(*)) PES is accessed directly. The second is assumed to involve radiationless transfer to the ground state, most probably by successive 2 (1)A(') right arrow-wavy 1 (1)A(") right arrow-wavy X (1)A(') couplings, mediated by conical intersections between the relevant PESs and the subsequent unimolecular decay of the resulting highly vibrationally excited ground state molecules yielding slow H atoms.

Journal Article↗
PubMed1995

Modeling direction selectivity of simple cells in striate visual cortex within the framework of the canonical microcircuit.

Nearly all models of direction selectivity (DS) in visual cortex are based on feedforward connection schemes, where geniculate input provides all excitatory synaptic input to both pyramidal and inhibitory neurons. Feedforward inhibition then suppresses feedforward excitation for nonoptimal stimuli. Anatomically, however, the majority of asymmetric, excitatory, synaptic contacts onto cortical cells is provided by other cortical neurons, as embodied in the Canonical Microcircuit of Douglas and Martin (1991). In this view, weak geniculate input is strongly amplified in the preferred direction by the action of intracortical excitatory connections, while in the null direction inhibition reduces geniculate-induced excitation. We investigate analytically and through biologically realistic computer simulations the functioning of a cortical network based on massive excitatory, cortico-cortical feedback. The behavior of this network is compared to physiological data as well as to the behavior of a purely feedforward model of DS based on nonlagged input. Our model explains a number of puzzling features of direction selective simple cells, including the small somatic input conductance changes that have been measured experimentally during stimulation in the null direction, and the persistence of DS while fully blocking inhibition in a single cell. Although the operation at the heart of our network is amplification, the network passes the linearity test of (Jagadeesh et al., 1993). We make specific predictions concerning the effect of selective blockade of cortical inhibition on the velocity-response curve.

Animals↗
PubMed2005

Connexin45 mediates gap junctional coupling of bistratified ganglion cells in the mouse retina.

Direction selectivity, a key feature of visual perception, originates in the retina and is transmitted by bistratified ganglion cells that, in the rabbit retina, exhibit a particular coupling pattern. We intracellularly labeled ganglion cells in different transgenic mouse lines, allowing a morphological classification of bistratified ganglion cells, an analysis of their coupling pattern, and the molecular identification of the connexins responsible for the coupling. Based on dendritic characteristics including co-fasciculation with the dendrites of cholinergic starburst amacrine cells, we were able to distinguish three types of bistratified ganglion cells. Two of these co-fasciculate with starburst amacrine cells and exhibit a specific homologous coupling pattern. Connexin45 (Cx45) appears to be the major component of the gap junctional channels because tracer coupling is absent in Cx45-deficient animals whereas it persists in Cx36-deficient animals. It is speculated that the transjunctional voltage dependence of Cx45 channels could support the transmission of direction selectivity.

Animals↗
PubMed2001

The insecticide target in the PSST subunit of complex I.

Current insecticides have been selected by sifting and winnowing hundreds of thousands of synthetic chemicals and natural products to obtain commercial preparations of optimal effectiveness and safety. This process has often ended up with compounds of high potency as inhibitors of the electron transport chain and more specifically of complex I (NADH:ubiquinone oxidoreductase). Many classes of chemicals are involved and the enzyme is one of the most complicated known, with 43 subunits catalyzing electron transfer from NADH to ubiquinone through flavin mononucleotide and up to eight iron-sulfur clusters. We used a potent photoaffinity ligand, (trifluoromethyl)diazirinyl[3H]pyridaben, to localize the insecticide target to a single high-affinity site in the PSST subunit that couples electron transfer from iron-sulfur cluster N2 to ubiquinone. Most importantly, all of the potent complex I-inhibiting pesticides, despite their great structural diversity, compete for this same specific binding domain in PSST. Finding their common mode of action and target provides insight into shared toxicological features and potential selection for resistant pests.

Animals↗
PubMed1994

A cosmid with a HyR marker for fungal library construction and screening.

The construction of a double-cos-site cosmid vector, pMOcosX, for use in making filamentous fungal genomic DNA libraries, is described. The vector has features that allow for selection of clones introduced into fungi by transformation and for efficient chromosome walking experiments. These features include (i) two cos sites allowing for easy construction of libraries without requiring size selection of insert DNA; (ii) an XhoI site for insertion of Sau3AI or MboI partially digested genomic DNA inserts that allows usage of a half-site fill-in method which minimizes the possibility of producing clones containing chimeric inserts; (iii) a bacterial hygromycin phosphotransferase-encoding gene fused to a modified cpc-1 promoter of Neurospora crassa for direct selection of cosmid clones upon introduction into fungal cells; and (iv) T7 and T3 bacteriophage promoters and EcoRI, NotI and BamHI restriction sites flanking the cloning site that allow for synthesis of, or isolation of, end-specific probes for chromosome walking. The combination of features in this vector allows for the easy construction and use of high-quality fungal DNA libraries from small amounts of genomic DNA.

Ascomycota↗
PubMed2002

Primary angioplasty and selection bias inpatients presenting late (>12 h) after onset of chest pain and ST elevation myocardial infarction.

OBJECTIVES: This study was designed to compare the in-hospital outcome of patients presenting with >12 h from onset of chest pain and acute ST elevation myocardial infarction (AMI) who received either immediate invasive or conservative therapy. BACKGROUND: The benefits of fibrinolytic therapy diminish in patients presenting with AMI and onset of chest pain >12 h. Primary angioplasty has been suggested as a possible treatment for such patients, but they have been excluded from most trials of primary angioplasty. It remains unclear if an invasive treatment strategy is beneficial to these patients. METHODS: Patients presenting with >12 h of chest pain and AMI were identified from the National Registry of Myocardial Infarction 2 database. Patients receiving invasive therapy <6 h after hospital admission were compared with those receiving conservative therapy. Short-term outcomes were compared on the basis of the initial therapy received. To help control for baseline differences in the groups, patients were matched with controls by propensity score methodology. RESULTS: On preliminary analysis, in-hospital outcome was improved in terms of recurrent ischemia, angina, myocardial infarction and mortality in patients receiving initial invasive therapy (odds ratio [OR] = 0.67; 95% confidence interval [CI] 0.49 to 0.92 for mortality). After matching by propensity score, the mortality benefit persisted on bivariate analysis (3.5% vs. 5.0%, p = 0.036), though on multivariate analysis, only a non-significant but strong trend toward decreased mortality remained (OR = 0.73; 95% CI 0.53 to 1.01). CONCLUSIONS: Patients receiving early invasive therapy had lower risk features on presentation. Selection bias may play an important role in choosing these patients' course of treatment and their subsequent outcomes. Certain patients presenting with AMI and duration of chest pain >12 h may benefit from early invasive therapy. These patients could be characterized in a randomized trial.

Aged↗