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At least 1,063 records · Page 59Linked to original sources
PubMed2005

Input of orexin/hypocretin neurons revealed by a genetically encoded tracer in mice.

The finding of orexin/hypocretin deficiency in narcolepsy patients suggests that this hypothalamic neuropeptide plays a crucial role in regulating sleep/wakefulness states. However, very little is known about the synaptic input of orexin/hypocretin-producing neurons (orexin neurons). We applied a transgenic method to map upstream neuronal populations that have synaptic connections to orexin neurons and revealed that orexin neurons receive input from several brain areas. These include the amygdala, basal forebrain cholinergic neurons, GABAergic neurons in the preoptic area, and serotonergic neurons in the median/paramedian raphe nuclei. Monoamine-containing groups that are innervated by orexin neurons do not receive reciprocal connections, while cholinergic neurons in the basal forebrain have reciprocal connections, which might be important for consolidating wakefulness. Electrophysiological study showed that carbachol excites almost one-third of orexin neurons and inhibits a small population of orexin neurons. These neuroanatomical findings provide important insights into the neural pathways that regulate sleep/wakefulness states.

Animals↗
PubMed2002

Genetic markers for study of the anopheline vectors of human malaria.

Human malaria is truly a disease of global proportions and is one of the most broadly distributed vector-borne infections. Anopheline mosquitoes are the exclusive vectors of human malaria. A handful of species predominate as the most notorious malaria vectors, but the species and forms involved in the transmission of human malaria world-wide are incredibly diverse. Many of the anophelines that vector malaria exist as members of species complexes that often contain vector and non-vector species. Additionally, single anopheline species often exhibit significant heterogeneity across the species' range. This phenotypic and genotypic plasticity exacerbates the difficulties in identification of vector populations and implementation of effective surveillance and control strategies. Polytene chromosome investigations were among the first to provide researchers with tangible genetic markers that could be used to differentiate between what are now recognised as species and chromosomal forms of anopheline mosquitoes. The advent of the polymerase chain reaction gave access to the molecular genetics of genomes and the techniques that followed have facilitated investigation of the genetics of individual specimens or population size samples. The variety and number of genetic markers available for the study of malaria vectors has literally exploded in the last 10 years. Markers have expanded from the 'traditional tools' to include a vast array of molecular markers. Contemporary markers range from what are now referred to as 'classical genetic markers' to methods used to detect and identify single nucleotide polymorphisms and finally to highly polymorphic markers. One of the greatest advantages of this wide variety of genetic markers is that researchers may choose to utilise any combination of markers or techniques to address multifaceted questions relating to malaria transmission. These molecular markers have proven useful in a wide variety of applications including molecular taxonomy, evolutionary systematics, population genetics, genetic mapping, and investigation of defined phenotypes.

Animals↗
PubMed2002

Experimental evidence for genetic recombination in the opportunistic pathogen Cryptosporidium parvum.

Cryptosporidium parvum is an intracellular protozoan parasite causing intestinal malabsorption and diarrhea in humans. The infection is usually self-limiting, although persistent cryptosporidosis is observed in immunocompromised and malnourished individuals. As with other Apicomplexa, the life cycle of Cryptosporidium is thought to comprise a sexual phase, during which a motile microgamont fuses with a sessile macrogamont. The four sporozoites found within each oocyst (the infectious form excreted in the feces) are thought to be the product of a meiotic division taking place immediately following fertilization, but the existence of a meiotic cycle in this genus has not been tested experimentally. To substantiate the occurrence of meiotic recombination in this species, we performed a genetic cross between two distinct isolates of C. parvum co-infected in INF-gamma knockout mice. We found that mixed infections produced recombinant progeny characterized by multilocus genotypes comprising alleles inherited from each parental line. This observation represents the first demonstration of sexual recombination in this pathogen. Together with the occurrence of genetically heterogeneous infections, this finding suggests that outcrossing between genotypes may occur in nature. Experimental crosses among Cryptosporidium populations will facilitate mapping of clinically relevant genes, the delineation of Cryptosporidium species, and defining the taxonomical status of C. parvum subtypes and host-specific genotypes.

Animals↗
PubMedDate not supplied

Neural networks with chaotic recursive nodes: techniques for the design of associative memories, contrast with Hopfield architectures, and extensions for time-dependent inputs.

This paper addresses the coding and storage of information in neural architectures with bifurcating recursive nodes that exhibit chaotic dynamics. It describes architectures of coupled recursive processing elements (RPEs) used to store binary strings, discusses the choices of network parameters related to the coding of zeros and ones, and analyzes several aspects of the network operation in implementing associative memories through populations of logistic maps. Experiments for the performance evaluation of these memories are described, and results addressing the operation under digital noise (flipped bits) and analog noise added to the prompting pattern are presented and analyzed. Quantitative aspects related to the representation of binary strings through cyclic states are equated, and then related to the planning and analysis of several experiments. A simple pre-processing procedure useful in situations of prompting conditions with analog noise is proposed, and the resultant increase in recovery performance presented. The performance of the RPEs associative networks is contrasted with the performance of Hopfield associative memories, and the situations where the RPEs networks present significant superiority are identified. An extended version of the proposed architecture, which allows to address the issues of time-dependent inputs and analog inputs, is analyzed in detail. Experimental results are presented, and the role of this extended architecture in providing mechanisms for modular RPEs architectures is pointed out.

Association Learning↗
PubMed1998

Experimental and Theoretical Studies of the Site Exchanges in Rh(4)(CO)(12) and IrRh(3)(CO)(12).

As observed by variable temperature and pressure (13)C NMR, the intramolecular scrambling of carbonyl ligands in Rh(4)(CO)(12) and IrRh(3)(CO)(12) is due to a merry-go-round process (3 &mgr;(2)-CO <--> 3 eta(1)-CO) about any triangular face of the metal tetrahedron. Both cluster compounds have a negative activation volume on going from the bridged ground-state structure of C(3)(v)() symmetry to an unbridged transition state, suggesting that bridged M-M distances are longer than unbridged M-M distances. Site exchange is faster in Rh(4)(CO)(12) than in IrRh(3)(CO)(12) where the apical position is occupied by an iridium atom. Density functional calculations on the bridged and unbridged forms of both cluster compounds have been made at two levels of approximation (LDA and GGA) including relativistic effects for Ir and Rh. LDA reproduces best the experimental distances and shows that opening bridges shortens the M-M bonds. The difference in volume of the bridged and unbridged forms of Rh(4)(CO)(12), as calculated from Connoly surfaces, agrees fairly well with the experimental activation volume. Calculations at the GGA level give the correct trends in energies. ELF maps and overlap population analysis indicate that iridium is more electropositive than rhodium, as suggested by the experimental results.

Journal Article↗
PubMed1998

dCAPS, a simple technique for the genetic analysis of single nucleotide polymorphisms: experimental applications in Arabidopsis thaliana genetics.

PCR-based detection of single nucleotide polymorphisms is a powerful tool for the plant geneticist. Cleaved amplified polymorphic sequence analysis is the most widely used approach for the detection of single nucleotide polymorphisms. However, this technique is limited to mutations which create or disrupt a restriction enzyme recognition site. This paper presents a modification of this technique where mismatches in a PCR primer are used to create a polymorphism based on the target mutation. This technique is useful for following known mutations in segregating populations and genetic mapping of isolated DNAs used for positional based cloning of new genes. In addition, a computer program has been developed that facilitates the design of these PCR primers.

Arabidopsis↗
PubMed2003

Defining equity in physical access to clinical services using geographical information systems as part of malaria planning and monitoring in Kenya.

Distance is a crucial feature of health service use and yet its application and utility to health care planning have not been well explored, particularly in the light of large-scale international and national efforts such as Roll Back Malaria. We have developed a high-resolution map of population-to-service access in four districts of Kenya. Theoretical physical access, based upon national targets, developed as part of the Kenyan health sector reform agenda, was compared with actual health service usage data among 1668 paediatric patients attending 81 sampled government health facilities. Actual and theoretical use were highly correlated. Patients in the larger districts of Kwale and Makueni, where access to government health facilities was relatively poor, travelled greater mean distances than those in Greater Kisii and Bondo. More than 60% of the patients in the four districts attended health facilities within a 5-km range. Interpolated physical access surfaces across districts highlighted areas of poor access and large differences between urban and rural settings. Users from rural communities travelled greater distances to health facilities than those in urban communities. The implications of planning and monitoring equitable delivery of clinical services at national and international levels are discussed.

Child↗
PubMed2001

Turkish variant late infantile neuronal ceroid lipofuscinosis (CLN7) may be allelic to CLN8.

One variant form of late infantile neuronal ceroid lipofuscinosis (LINCL) is found predominantly within the Turkish population (CLN7). Exclusion mapping showed that CLN7 was not an allelic variant of known NCL loci (CLN1, CLN2, CLN3, CLN5 or CLN6). Using the method of homozygosity mapping, a genome-wide search was undertaken and a total of 358 microsatellite markers were typed at an average distance of about 10 cM. A region of shared homozygosity was identified on chromosome 8p23. This telomeric region contained the recently identified CLN8 gene. A missense mutation in CLN8 causes progressive epilepsy with mental retardation (EPMR) or Northern epilepsy, which has so far been reported only from Finland and is now classified as an NCL. The mouse model mnd has been shown to carry a 1 bp insertion in the orthologous Cln8 gene. Statistically significant evidence for linkage was obtained in this region, with LOD scores > 3, assuming either homogeneity or heterogeneity. Flanking recombinants defined a critical region of 14 cM between D8S504 and D8S1458 which encompasses CLN8. This suggests that Turkish variant LINCL, despite having an earlier onset and more severe phenotype, may be an allelic variant of Northern epilepsy. However mutation analysis has not so far identified a disease causing mutation within the coding or non-coding exons of CLN8 in the families. The Turkish variant LINCL disease-causing mutation remains to be delineated.

Alleles↗
PubMed1984

Dynamic interactions of fluorescently labeled microtubule-associated proteins in living cells.

Microtubule-associated proteins (MAPs) from calf brain were fluorescently labeled with 6-iodoacetamido fluorescein (I-AF). The modified MAPs (especially enriched for MAP2) were fully active in promoting tubulin polymerization in vitro and readily associated with cytoplasmic filaments when microinjected into living cultured cells. Double-labeling experiments indicated that the microinjected AF-MAPs were incorporated predominantly, if not exclusively, into cytoplasmic microtubules in untreated cells or paracrystals induced within vinblastine-treated cells. Similar results were obtained with different cell types (neuronal, epithelial, and fibroblastic) of diverse origin (man, mouse, chicken, and rat kangaroo). Mobility measurements of the microinjected AF-MAPs using the method of fluorescence-photobleaching recovery (FPR) revealed two populations of AF-MAPs with distinct dynamic properties: One fraction represents the soluble pool of MAPs and is mobile with a diffusion coefficient of D = 3 X 10(-9) cm2/s. The other fraction of MAPs is associated with the microtubules and is essentially immobile on the time scale of FPR experiments. However, it showed slow fluorescence recovery with an apparent half time of approximately 5 min. The slow recovery of fluorescence on defined photobleached microtubules occurred most probably by the incorporation of AF-MAPs from the soluble cytoplasmic pool into the bleached area. The bleached spot on defined microtubules remained essentially immobile during the slow recovery phase. These results suggest that MAPs can associate in vivo with microtubules of diverse cell types and that treadmilling of MAP2-containing microtubules in vivo, if it exists, is slower than 4 micron/h.

Animals↗
PubMed2006

Statistical methods in genetics.

In recent years, a very large variety of statistical methodologies, at various levels of complexity, have been put forward to analyse genotype data and detect genetic variations that may be responsible for increasing the susceptibility to disease. This review provides a concise account of a number of selected statistical methods for population-based association mapping, from single-marker tests of association to multi-marker data mining techniques for gene-gene interaction detection.

Genetic Markers↗
PubMed1992

Genetic changes accompanying increased fitness in evolving populations of Escherichia coli.

Two populations of Escherichia coli, each initiated with a single clone containing a derivative of the plasmid pBR322, were maintained for long periods in glucose-limited continuous culture. In both populations, after an extensive number of generations had elapsed, clones were isolated in which the transposon Tn3 from the plasmid had integrated into the bacterial chromosome. In both cases examined, the transpositions were shown to increase relative fitness approximately 6-7%, in the environment in which the populations were maintained. The loci of integration were mapped to approximately 13.2 min (population 1) and approximately 32.8 min (population 2).

Biological Evolution↗
PubMed2001

PlasmoDB: An integrative database of the Plasmodium falciparum genome. Tools for accessing and analyzing finished and unfinished sequence data. The Plasmodium Genome Database Collaborative.

The PLASMODIUM: falciparum Genome Database (http://PlasmoDB.org) integrates sequence information, automated analyses and annotation data emerging from the P.falciparum genome sequencing consortium. To date, raw sequence coverage is available for >90% of the genome, and two chromosomes have been finished and annotated. Data in PlasmoDB are organized by chromosome (1-14), and can be accessed using a variety of tools for graphical and text-based browsing or downloaded in various file formats. The GUS (Genomics Unified Schema) implementation of PlasmoDB provides a multi-species genomic relational database, incorporating data from human and mouse, as well as P.falciparum. The relational schema uses a highly structured format to accommodate diverse data sets related to genomic sequence and gene expression. Tools have been designed to facilitate complex biological queries, including many that are specific to PLASMODIUM: parasites and malaria as a disease. Additional projects seek to integrate genomic information with the rich data sets now becoming available for RNA transcription, protein expression, metabolic pathways, genetic and physical mapping, antigenic and population diversity, and phylogenetic relationships with other apicomplexan parasites. The overall goal of PlasmoDB is to facilitate Internet- and CD-ROM-based access to both finished and unfinished sequence information by the global malaria research community.

Animals↗
PubMed2001

Targeted development of informative microsatellite (SSR) markers.

We describe a novel approach, selectively amplified microsatellite (SAM) analysis, for the targeted development of informative simple sequence repeat (SSR) markers. A modified selectively amplified microsatellite polymorphic loci assay is used to generate multi-locus SSR fingerprints that provide a source of polymorphic DNA markers (SAMs) for use in genetic studies. These polymorphisms capture the repeat length variation associated with SSRs and allow their chromosomal location to be determined prior to the expense of isolating and characterising individual loci. SAMs can then be converted to locus-specific SSR markers with the design and synthesis of a single primer specific to the conserved region flanking the repeat. This approach offers a cost-efficient and rapid method for developing SSR markers for predetermined chromosomal locations and of potential informativeness. The high recovery rate of useful SSR markers makes this strategy a valuable tool for population and genetic mapping studies. The utility of SAM analysis was demonstrated by the development of SSR markers in bread wheat.

Alleles↗
PubMed1999

A haplotype-based study of lithium responding patients with bipolar affective disorder on the Faroe Islands.

The Faroe Islands are a small group of islands in the North Atlantic Ocean, situated between Norway, Iceland and Scotland. The origin of the population is thought to be a mixture of Norwegian, Danish and British. The islands were populated at the same time as Iceland, i.e. around 1100 years ago, and the size of the population was around, and occasionally below, 4000 inhabitants until 1800, after which it increased to its present-day level of around 45,000. The population is descended from Scandinavian and British ancestors. Because of the low number of founders and small size for many centuries, the Faroese population is perhaps the most valuable European population for genetic mapping of complex disease genes. The present study searched for haplotype sharing on chromosome 18 among eight lithium responding patients with bipolar affective disorder related, on average, 6.2 generations ago, using 30 DNA markers. In order to obtain as homogeneous a sample as possible, strict inclusion criteria based on severity of phenotype, geography and treatment response, were applied. Evidence suggestive of increased haplotype sharing on the distal part of chromosome 18q23 in the region implicated by Freimer and co-workers was found. However, methods of genetic analysis which might provide a conclusive result are not yet available.

Adolescent↗
PubMed2005

Selection in backcross programmes.

Backcrossing is a well-known and long established breeding scheme where a characteristic is introgressed from a donor parent into the genomic background of a recurrent parent. The various uses of backcrossing in modern genetics, particularly with the help of molecular markers, are reviewed here. Selection in backcross programmes is used to either improve the genetic value of plant and animal populations or fine map quantitative trait loci. Both cases are helpful in our understanding of the genetic bases of quantitative traits variation.

Animals↗
PubMed2006

Intra- and interpopulation genotype reconstruction from tagging SNPs.

The optimal method to be used for tSNP selection, the applicability of a reference LD map to unassayed populations, and the scalability of these methods to genome-wide analysis, all remain subjects of debate. We propose novel, scalable matrix algorithms that address these issues and we evaluate them on genotypic data from 38 populations and four genomic regions (248 SNPs typed for approximately 2000 individuals). We also evaluate these algorithms on a second data set consisting of genotypes available from the HapMap database (1336 SNPs for four populations) over the same genomic regions. Furthermore, we test these methods in the setting of a real association study using a publicly available family data set. The algorithms we use for tSNP selection and unassayed SNP reconstruction do not require haplotype inference and they are, in principle, scalable even to genome-wide analysis. Moreover, they are greedy variants of recently developed matrix algorithms with provable performance guarantees. Using a small set of carefully selected tSNPs, we achieve very good reconstruction accuracy of "untyped" genotypes for most of the populations studied. Additionally, we demonstrate in a quantitative manner that the chosen tSNPs exhibit substantial transferability, both within and across different geographic regions. Finally, we show that reconstruction can be applied to retrieve significant SNP associations with disease, with important genotyping savings.

Algorithms↗
PubMed2006

Identification of QTL controlling root growth response to phosphate starvation in Arabidopsis thaliana.

One of the responses of plants to low sources of external phosphorus (P) is to modify root architecture. In Arabidopsis thaliana plantlets grown on low P, the primary root length (PRL) is reduced whereas lateral root growth is promoted. By using the Bay-0 x Shahdara recombinant inbred line (RIL) population, we have mapped three quantitative trait loci (QTL) involved in the root growth response to low P. The Shahdara alleles at these three QTL promote the response of the primary root to low P (i.e., root length reduction). One of these QTL, LPR1, located in a 2.8 Mb region at the top of chromosome 1, explains 52% of the variance of the PRL. We also detected a single QTL associated with primary root cell elongation in response to low P which colocalizes with LPR1. LPR1 does not seem to be involved in other typical P-starvation responses such as growth and density of root hairs, excretion of acid phosphatases, anthocyanin accumulation or the transcriptional induction of the P transporter Phtl;4. LPR1 might highlight new aspects of root growth that are revealed specifically under low P conditions.

Alleles↗
PubMed1997

Immunohistochemical localization of mast cells and mast cell-nerve interactions in oral lichen planus.

OBJECTIVES: Mast cell mediators are likely to be involved in at least some aspects of the immunopathogenesis of oral lichen planus (OLP). The aim of this project was to map mast cell populations in OLP and identify possible sites of mast cell-nerve interactions. MATERIALS AND METHODS: Monoclonal antibodies specific for tryptase and neurofilaments were used to identify mast cells and nerves respectively in an immunohistochemical study of OLP (n = 25) and normal oral buccal mucosa (NOBM) (n = 13) using a double-labelling protocol. Data analysis used paired t-test, multiway analysis of variance and Wilcoxon rank tests. RESULTS: Morphometric analyses showed the greatest mast cell density in the most superficial of the three depth layers examined in OLP, an increase of 130% compared with NOBM. Mast cells associated with neurofilaments ranged from 21.9% in OLP to 10.2% in NOBM. Mean epithelial thickness was significantly lower in OLP (P < 0.001) but without a strong correlation with mast cell density. CONCLUSIONS: Increased mast cell and mast cell-nerve interactions in OLP suggest both a controlling role over the lesional cell populations and a secondary role to the immune response once this becomes established.

Analysis of Variance↗