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PubMed2006

DNA microarray analysis of striatal gene expression in symptomatic transgenic Huntington's mice (R6/2) reveals neuroinflammation and insulin associations.

Huntington's disease (HD) is an inherited, progressive neurodegenerative disorder caused by CAG repeat expansion in the gene that codes for the protein huntingtin. The underlying neuropathological events leading to the selectivity of striatal neuronal loss are unknown. However, the huntingtin mutation interferes at several levels of normal cell function. The complexity of this disease makes microarray analysis an appealing technique to begin the identification of common pathways that may contribute to the pathology. In this study, striatal tissue was extracted for gene expression profiling from wild-type and symptomatic transgenic Huntington mice (R6/2) expressing part of the human Huntington's disease gene. We interrogated a 15 K high-density mouse EST array not previously used for HD and identified 170 significantly differentially expressed ESTs in symptomatic R6/2 mice. Of the 80 genes with known function, 9 genes had previously been identified as altered in HD. 71 known genes were associated with HD for the first time. The data obtained from this study confirm and extend previous observations using DNA microarray techniques on genetic models for HD, revealing novel changes in expression in a number of genes not previously associated with HD. Further bioinformatic analysis, using software to construct biological association maps, focused attention on proteins such as insulin and TH1-mediated cytokines, suggesting that they may be important regulators of affected genes. These results may provide insight into the regulation and interaction of genes that contribute to adaptive and pathological processes involved in HD.

Animals↗
PubMed2006

RGS2 is upregulated by and attenuates the hypertrophic effect of alpha1-adrenergic activation in cultured ventricular myocytes.

Regulator of G protein signaling (RGS) proteins counter the effects of G protein-coupled receptors (GPCRs) by limiting the abilities of G proteins to propagate signals, although little is known concerning their role in cardiac pathophysiology. We investigated the potential role of RGS proteins on alpha1-adrenergic receptor signals associated with hypertrophy in primary cultures of neonatal rat cardiomyocytes. Levels of mRNA encoding RGS proteins 1-5 were examined, and the alpha1-adrenergic agonist phenylephrine (PE) significantly increased RGS2 gene expression but had little or no effect on the others. The greatest changes in RGS2 mRNA occurred within the first hour of agonist addition. We next investigated the effects of RGS2 overexpression produced by infecting cells with an adenovirus encoding RGS2-cDNA on cardiomyocyte responses to PE. As expected, PE increased cardiomyocyte size and also significantly upregulated alpha-skeletal actin and ANP expression, the markers of hypertrophy, as well as the Na-H exchanger 1 isoform. These effects were blocked in cells infected with the adenovirus expressing RGS2. We also examined hypertrophy-associated MAP kinase pathways, and RGS2 overexpression completely prevented the activation of ERK by PE. In contrast, the activation of both JNK and p38 unexpectedly were increased by RGS2, although the ability of PE to further activate the p38 pathway was reduced. These results indicate that RGS2 is an important negative-regulatory factor in cardiac hypertrophy produced by alpha1-adrenergic receptor stimulation through complex mechanisms involving the modulation of mitogen-activated protein kinase signaling pathways.

Animals↗
PubMed2006

The American Association for Pediatric Ophthalmology and Strabismus workforce distribution project.

PURPOSE: To describe data sources and functional utility of the American Association for Pediatric Ophthalmology and Strabismus (AAPOS) workforce database and associated map files. METHODS: Population data from the 2000 U.S. Census and current listings from the AAPOS and American Academy of Ophthalmology (AAO) databases were organized to demonstrate and analyze practitioner-to-population relationships for metropolitan statistical areas nationwide. An interactive map was developed to provide an intuitive graphical display of the data. RESULTS: A total of 749 active AAPOS members were distributed in 154 of 280 defined metropolitan statistical areas. Within these areas, a 0- to 20-year age subgroup varied from 17.8% to 42.6%, with an average of 30.4%. The AAPOS member-to-million-person ratio varied from 1.3 to 27, with higher numbers generally representing regions with population bases inadequately defined by Census Bureau statistical area definitions. Ratios for a majority of larger, better-defined areas ranged from 3 to 4 AAPOS members per million persons. Sizable areas with no AAPOS member presence were identified and tabulated. AAO members with a specified pediatric practice focus who were not AAPOS members were identified in 103 areas, possibly influencing patient choices and practitioner referrals for these regions. CONCLUSIONS: The AAPOS workforce database and related interactive map display practitioner and population data that may assist physicians and planners in targeting practice development and identifying potentially underserved areas.

Databases, Factual↗
PubMed2005

A proton pumping pyrophosphatase in acidocalcisomes of Herpetomonas sp.

Acidocalcisomes are acidic calcium storage organelles found in several microorganisms. They are characterized by their acidic nature, high electron density, high content of polyphosphates and several cations. Electron microscopy contrast tuned images of Herpetomonas sp. showed the presence of several electron dense organelles ranging from 100 to 300 nm in size. In addition, X-ray element mapping associated with energy-filtering transmission electron microscopy showed that most of the cations, namely Na, Mg, P, K, Fe and Zn, are located in their matrix. Using acridine orange as an indicator dye, a pyrophosphate-driven H+ uptake was measured in cells permeabilized by digitonin. This uptake has an optimal pH of 6.5-6.7 and was inhibited by sodium fluoride (NaF) and imidodiphosphate (IDP), two H+-pyrophosphatase inhibitors. H+ uptake was not promoted by ATP. Addition of 50 microM Ca2+ induced the release of H+, suggesting the presence of a Ca2+/H+ countertransport system in the membranes of the acidic compartments. Na+ was unable to release protons from the organelles. The pyrophosphate-dependent H+ uptake was dependent of ion K+ and inhibited by Na+ Herpetomonas sp. immunolabeled with monoclonal antibodies raised against a Trypanosoma cruzi V-H+-pyrophosphatase shows intense fluorescence in cytoplasmatic organelles of size and distribution similar to the electron-dense vacuoles. Together, these results suggest that the electron dense organelles found in Herpetomonas sp. are homologous to the acidocalcisomes described in other trypanosomatids. They possess a vacuolar H+-pyrophosphatase and a Ca2+/H+ antiport. However, in contrast to the other trypanosomatids so far studied, we were not able to measure any ATP promoted H+ transport in the acidocalcisomes of this parasite.

Animals↗
PubMed2005

Predictive neural networks for gene expression data analysis.

Gene expression data generated by DNA microarray experiments have provided a vast resource for medical diagnosis and disease understanding. Most prior work in analyzing gene expression data, however, focuses on predictive performance but not so much on deriving human understandable knowledge. This paper presents a systematic approach for learning and extracting rule-based knowledge from gene expression data. A class of predictive self-organizing networks known as Adaptive Resonance Associative Map (ARAM) is used for modelling gene expression data, whose learned knowledge can be transformed into a set of symbolic IF-THEN rules for interpretation. For dimensionality reduction, we illustrate how the system can work with a variety of feature selection methods. Benchmark experiments conducted on two gene expression data sets from acute leukemia and colon tumor patients show that the proposed system consistently produces predictive performance comparable, if not superior, to all previously published results. More importantly, very simple rules can be discovered that have extremely high diagnostic power. The proposed methodology, consisting of dimensionality reduction, predictive modelling, and rule extraction, provides a promising approach to gene expression analysis and disease understanding.

Animals↗
PubMed2004

Corn and humans: recombination and linkage disequilibrium in two genomes of similar size.

Two species with genomes of almost identical size, maize and human, have different evolutionary histories, and as a result their genomes differ greatly in their content of retroelements, average size of the genes and amount of genetic diversity. However, there are also significant similarities: they both have undergone bottlenecks during their recent history and seem to have non-uniform distribution of recombination events. The human genome has been shown to contain large linkage blocks characterized by a limited number of haplotypes. A similar linkage block structure is likely to exist in maize. Although highly diverse maize populations show rapid decline of linkage disequilibrium, as in humans, it is possible to define populations with strong linkage disequilibrium, suitable for whole-genome scan association mapping. The genetic diversity and lack of sequence homology found in maize influences recombinational properties and local linkage disequilibrium levels but also challenges our understanding of the relationship between the genome sequence and species definition.

Alleles↗
PubMed2001

Age-related maculopathy: an expanded genome-wide scan with evidence of susceptibility loci within the 1q31 and 17q25 regions.

PURPOSE: We seek to identify genetic loci that contribute to age-related maculopathy susceptibility. METHODS: Families consisting of at least two siblings affected by age-related maculopathy were ascertained using eye care records and fundus photographs. Additional family members were used to increase the power to detect linkage. Microsatellite genotyping was conducted by the National Heart, Lung and Blood Institute Mammalian Genotyping Service and the National Institutes of Health Center for Inherited Disease Research. Linkage analyses were conducted with parametric (autosomal dominant; heterogeneity lod score) and nonparametric methods (S(all) statistic) using three diagnostic models. False-positive rates were determined from simulations using actual pedigrees and genotyping data. RESULTS: Under our least stringent diagnostic model, model C, 860 affected individuals from 391 families (452 sib pairs) were genotyped. Sixty-five percent of the affected individuals had evidence of exudative disease. Four regions, 1q31, 9p13, 10q26, and 17q25, showed multipoint heterogeneity lod scores or S(all) scores of 2.0 or greater (under at least one model). Under our most stringent diagnostic model, model A, the 1q31 heterogeneity lod score was 2.46 between D1S1660 and D1S1647. Under model C, the 17q25 heterogeneity lod score at D17S928 was 3.16. Using a threshold of 1.5, additional loci on chromosomes 2 and 12 were identified. CONCLUSIONS: The locus on chromosome 1q31 independently confirms a report by Klein and associates mapping an age-related maculopathy susceptibility gene to this region. Simulations indicate that the 1q31 and 17q25 loci are unlikely to be false positives. There was no evidence that other known macular or retinal dystrophy candidate gene regions are major contributors to the genetics of age-related maculopathy.

Aged↗
PubMed1999

Nuclear shuttling of yeast scaffold Ste5 is required for its recruitment to the plasma membrane and activation of the mating MAPK cascade.

Localization of Ste5 to GP at the plasma membrane is essential for transmission of the pheromone signal to associated MAP kinase cascade enzymes. Here, we show that this crucial localization requires prior shuttling of Ste5 through the nucleus. Ste5 shuttles through the nucleus constitutively during vegetative growth. Pheromone enhances nuclear export of Ste5, and this pool translocates vectorially to the cell periphery. Remarkably, Ste5 that cannot transit the nucleus is unable to localize at the periphery and activate the pathway, while Ste5 with enhanced transit through the nucleus has enhanced ability to localize to the periphery and activate the pathway. This novel regulatory scheme may ensure that cytoplasmic Ste5 does not activate downstream kinases in the absence of pheromone and could be applicable to other membrane-recruited signaling proteins.

Adaptor Proteins, Signal Transducing↗
PubMed1998

Epithelial and fibroblastoid cells contain numerous cell-type specific putative microtubule-regulating proteins, among which are ezrin and fodrin.

Upon cell junction formation, the microtubules of polarizing epithelial cells become reorganized by unknown signaling mechanisms and regulating proteins. Microtubule-associated (MAPs) and other types of proteins are likely to be involved in this process, but most of these are unknown. Such proteins are called here collectively microtubule-regulating proteins (MRPs). As a first step towards their characterization, we used co-sedimentation of cytosolic proteins of MDCK cells and A72, a dog fibroblastoid line, with an excess of taxol-stabilized MTs, to obtain a cell fraction enriched in putative MRPs ("MRPs"). Additional tests have led to the inventory of around 40 "MRPs" among the 80 proteins present in the microtubule pellet. We also found that "MRPs" are recovered in higher amounts from MDCK cytosol, and that half of these are cell-type specific. These results corroborate data from yeast cells and insect eggs, and show that in mammalian somatic cells too, a large number of proteins seems to be involved in microtubule regulation, and that different cell types use a specific set of MRPs. "MRPs" found in both cell types are the intermediate chain of cytoplasmic dynein, Arp1, the major subunit of the dynactin complex, and CLIP-170. Two MDCK-specific "MRPs" were identified as the actin-binding proteins ezrin and alpha-fodrin. These results are discussed with regard to a possible involvement of ezrin and fodrin in morphogenetic interactions of microtubules with the membrane cytoskeleton in polarizing epithelia upon junction formation.

Actins↗
PubMed1997

Supervised Learning Extensions to the CLAM Network.

The contextual layered associative memory (CLAM) has been developed as a self-generating structure which implements a probabilistic encoding scheme. The training algorithms are geared towards the unsupervised generation of a layerable associative mapping ([Thacker and Mayhew, 1989]). We show here that the resulting structure will support layers which can be trained to produce outputs that approximate conditional probabilities of classification. Unsupervised and supervised learning algorithms operate independently permitting the unsupervised representational layer to be developed before supervision is available. The system thus supports learning which is inherently more flexible than conventional node labelling schemes. Copyright 1997 Elsevier Science Ltd. All Rights Reserved.

Journal Article↗
PubMed1998

Efficient Learning of VAM-Based Representation of 3D Targets and its Active Vision Applications.

There has been a considerable interest in using active vision for various applications. This interest is primarily because active vision can enhance machine vision capabilities by dynamically changing the camera parameters based on the content of the scene. An important issue in active vision is that of representing 3D targets in a manner that is invariant to changing camera configurations. This paper addresses this representation issue for a robotic active vision system. An efficient Vector Associative Map (VAM)-based learning scheme is proposed to learn a joint-based representation. Computer simulations and experiments are first performed to evaluate the effectiveness of this scheme using the University of Illinois Active Vision System (UIAVS). The invariance property of the learned representation is then exploited to develop several robotic applications. These include, detecting moving targets, saccade control, planning saccade sequences and controlling a robot manipulator.

Journal Article↗
PubMed2001

Why is there so little intragenic linkage disequilibrium in humans?

The efficient design of association mapping studies relies on a knowledge of the rate of decay of linkage disequilibrium with distance. This rate depends on the population recombination rate, C. An estimate of C for humans is usually obtained from a comparison of physical and genetic maps, assuming an effective population size of approximately 10(4). We demonstrate that under both a constant population size model and a model of long-term exponential growth, there is evidence for more recombination in polymorphism data than is expected from this estimate. An important contribution of gene conversion to meiotic recombination helps to explain our observation, but does not appear to be sufficient. The occurrence of multiple hits at CpG sites and the presence of population structure are not explanations.

Chromosome Mapping↗
PubMed2006

Modeling of the polluting emissions from a cement production plant by partial least-squares, principal component regression, and artificial neural networks.

A Portland cement process was taken into consideration and monitored for one month with respect to polluting emissions, fuel and raw material physical-chemical properties, and operative conditions. Soft models, based on linear (partial least-squares, PLS, and principal component regression, PCR) and nonlinear (artificial neural networks, ANNs) approaches, were employed to predict the polluting emissions. The predictive ability of the three regression methods was evaluated by means of the partition of the dataset by Kohonen self-associative maps into both a training and a test set. Then, a "leave-more-out" approach, based on the use of a training set, a test set, and a production set, was adopted. The training set was used to build the models, the test set was used to select the number of latent variables or the neural network training endpoint, and the production set was used to produce genuine predictions. ANNs proved to be much more effective in prediction with respect to PLS and PCR and, at least in the case of SO2 and dust, provided a predictive ability comparable with the experimental estimated uncertainty of the response. This showed that it is possible to satisfactorily predict the two responses. Such a prediction will result in the prevention of environmental and legal problems connected to the polluting emissions.

Air Pollution↗
PubMed2003

Consolidation during sleep of perceptual learning of spoken language.

Memory consolidation resulting from sleep has been seen broadly: in verbal list learning, spatial learning, and skill acquisition in visual and motor tasks. These tasks do not generalize across spatial locations or motor sequences, or to different stimuli in the same location. Although episodic rote learning constitutes a large part of any organism's learning, generalization is a hallmark of adaptive behaviour. In speech, the same phoneme often has different acoustic patterns depending on context. Training on a small set of words improves performance on novel words using the same phonemes but with different acoustic patterns, demonstrating perceptual generalization. Here we show a role of sleep in the consolidation of a naturalistic spoken-language learning task that produces generalization of phonological categories across different acoustic patterns. Recognition performance immediately after training showed a significant improvement that subsequently degraded over the span of a day's retention interval, but completely recovered following sleep. Thus, sleep facilitates the recovery and subsequent retention of material learned opportunistically at any time throughout the day. Performance recovery indicates that representations and mappings associated with generalization are refined and stabilized during sleep.

Humans↗
PubMed2006

Magnitude and distribution of linkage disequilibrium in population isolates and implications for genome-wide association studies.

The genome-wide distribution of linkage disequilibrium (LD) determines the strategy for selecting markers for association studies, but it varies between populations. We assayed LD in large samples (200 individuals) from each of 11 well-described population isolates and an outbred European-derived sample, using SNP markers spaced across chromosome 22. Most isolates show substantially higher levels of LD than the outbred sample and many fewer regions of very low LD (termed 'holes'). Young isolates known to have had relatively few founders show particularly extensive LD with very few holes; these populations offer substantial advantages for genome-wide association mapping.

Chromosomes, Human, Pair 22↗
PubMed2006

A worldwide survey of haplotype variation and linkage disequilibrium in the human genome.

Recent genomic surveys have produced high-resolution haplotype information, but only in a small number of human populations. We report haplotype structure across 12 Mb of DNA sequence in 927 individuals representing 52 populations. The geographic distribution of haplotypes reflects human history, with a loss of haplotype diversity as distance increases from Africa. Although the extent of linkage disequilibrium (LD) varies markedly across populations, considerable sharing of haplotype structure exists, and inferred recombination hotspot locations generally match across groups. The four samples in the International HapMap Project contain the majority of common haplotypes found in most populations: averaging across populations, 83% of common 20-kb haplotypes in a population are also common in the most similar HapMap sample. Consequently, although the portability of tag SNPs based on the HapMap is reduced in low-LD Africans, the HapMap will be helpful for the design of genome-wide association mapping studies in nearly all human populations.

Chromosome Mapping↗
PubMed2001

Identifying regulatory networks by combinatorial analysis of promoter elements.

Several computational methods based on microarray data are currently used to study genome-wide transcriptional regulation. Few studies, however, address the combinatorial nature of transcription, a well-established phenomenon in eukaryotes. Here we describe a new approach using microarray data to uncover novel functional motif combinations in the promoters of Saccharomyces cerevisiae. In addition to identifying novel motif combinations that affect expression patterns during the cell cycle, sporulation and various stress responses, we observed regulatory cross-talk among several of these processes. We have also generated motif-association maps that provide a global view of transcription networks. The maps are highly connected, suggesting that a small number of transcription factors are responsible for a complex set of expression patterns in diverse conditions. This approach may be useful for modeling transcriptional regulatory networks in more complex eukaryotes.

Cell Cycle↗
PubMed2005

X-chromosome as a marker for population history: linkage disequilibrium and haplotype study in Eurasian populations.

Linkage disequilibrium (LD) structure is still unpredictable because the interplay of regional recombination rate and demographic history is poorly understood. We have compared the distribution of LD across two genomic regions differing in crossing-over activity -- Xq13 (0.166 cM/Mb) and Xp22 (1.3 cM/Mb) -- in 15 Eurasian populations. Demographic events predicted to increase the LD level -- genetic drift, bottleneck and admixture - had a very strong impact on extent and patterns of regional LD across Xq13 compared to Xp22. The haplotype distribution of the DXS1225-DXS8082 microsatellites from Xq13 exhibiting strong association in all populations was remarkably influenced by population history. European populations shared one common haplotype with a frequency of 25-40%. The Volga-Ural populations studied, living at the geographic borderline of Europe, showed elevated LD as well as harboring a significant fraction of haplotypes originating from East Asia, thus reflecting their past migrations and admixture. In the young Kuusamo isolate from Finland, a bottleneck has led to allelic associations between loci and shifted the haplotype distribution, but has much less affected single microsatellite allele frequencies compared to the main Finnish population. The data show that the footprint of a demographic event is longer preserved in haplotype distribution within a region of low crossing-over rate, than in the information content of a single marker, or between actively recombining markers. As the knowledge of LD patterns is often chosen to assist association mapping of common disease, our conclusions emphasize the importance of understanding the history, structure and variation of a study population.

Asia↗