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PubMed2006

Molecular characterization of human melanocortin-3 receptor ligand-receptor interaction.

UNLABELLED: Melanocortin-3 receptor (MC3R), primarily expressed in the hypothalamus, plays an important role in the regulation of energy homeostasis. MC3R-deficient (MC3R(-)(/)(-)) mice demonstrate increased fat mass, higher feeding efficiency, hyperleptinaemia, and mild hyperinsulinism. At least one specific mutation of MC3R has been identified to be associated with human obesity. Functional analysis of this altered MC3R (I183N) has indicated that the mutation completely abolishes agonist-mediated receptor activation. However, the specific molecular determinants of MC3R responsible for ligand binding and receptor signaling are currently unknown. The present study is to determine the structural aspects of MC3R responsible for ligand binding and receptor signaling. On the basis of our theoretical model for MC1R, using mutagenesis, we have examined 19 transmembrane domain amino acids selected for these potential roles in ligand binding and receptor signaling. Our results indicate that (i) substitutions of charged amino acid residues E131 in transmembrane domain 2 (TM2), D154 and D158 in TM3, and H298 in TM6 with alanine dramatically reduced NDP-MSH binding affinity and receptor signaling, (ii) substitutions of aromatic amino acids F295 and F296 in TM6 with alanine also significantly decreased NDP-MSH binding and receptor activity, (iii) substitutions of D121in TM2 and D332 in TM7 with alanine resulted in the complete loss of ligand binding, ligand induced receptor activation, and cell surface protein expression, and (iv) interestingly, substitution of L165 in TM3 with methionine or alanine switched antagonist SHU9119 into a receptor agonist. IN CONCLUSION: Our results suggest that TM3 and TM6 are important for NDP-MSH binding, while D121 in TM2 and D332 in TM7 are crucial for receptor activity and signaling. Importantly, L165 in TM3 is critical for agonist or antagonist selectivity. These results provide important information about the molecular determinants of hMC3R responsible for ligand binding and receptor signaling.

Amino Acid Sequence↗
PubMed2006

Ubiquitination-mediated protein degradation and modification: an emerging theme in plant-microbe interactions.

Post-translational modification is central to protein stability and to the modulation of protein activity. Various types of protein modification, such as phosphorylation, methylation, acetylation, myristoylation, glycosylation, and ubiquitination, have been reported. Among them, ubiquitination distinguishes itself from others in that most of the ubiquitinated proteins are targeted to the 26S proteasome for degradation. The ubiquitin/26S proteasome system constitutes the major protein degradation pathway in the cell. In recent years, the importance of the ubiquitination machinery in the control of numerous eukaryotic cellular functions has been increasingly appreciated. Increasing number of E3 ubiquitin ligases and their substrates, including a variety of essential cellular regulators have been identified. Studies in the past several years have revealed that the ubiquitination system is important for a broad range of plant developmental processes and responses to abiotic and biotic stresses. This review discusses recent advances in the functional analysis of ubiquitination-associated proteins from plants and pathogens that play important roles in plant-microbe interactions.

Models, Biological↗
PubMed2000

Molecular markers and their use in animal breeding.

The use of DNA markers to define the genetic makeup (genotype) and predict the performance of an animal is a powerful aid to animal breeding. One strategy is known as marker-assisted selection (MAS). MAS facilitates the exploitation of existing genetic diversity in breeding populations and can be used to improve a whole range of desirable traits. DNA markers are, by definition, polymorphic, and the methods used to define DNA markers include restriction fragment length polymorphisms (RFLPs), microsatellites, and single nucleotide polymorphisms (SNPs). Linkage analysis, association analysis and analysis of gene function can be used to determine which polymorphisms are useful markers for desirable traits. Future prospects include the use of high throughput DNA microarray (DNA chip) technology which could revolutionize animal breeding in the next millennium.

Animal Husbandry↗
PubMed2003

Identification of a tight junction-associated guanine nucleotide exchange factor that activates Rho and regulates paracellular permeability.

Rho family GTPases are important regulators of epithelial tight junctions (TJs); however, little is known about how the GTPases themselves are controlled during TJ assembly and function. We have identified and cloned a canine guanine nucleotide exchange factor (GEF) of the Dbl family of proto-oncogenes that activates Rho and associates with TJs. Based on sequence similarity searches and immunological and functional data, this protein is the canine homologue of human GEF-H1 and mouse Lfc, two previously identified Rho-specific exchange factors known to associate with microtubules in nonpolarized cells. In agreement with these observations, immunofluorescence of proliferating MDCK cells revealed that the endogenous canine GEF-H1/Lfc associates with mitotic spindles. Functional analysis based on overexpression and RNA interference in polarized MDCK cells revealed that this exchange factor for Rho regulates paracellular permeability of small hydrophilic tracers. Although overexpression resulted in increased size-selective paracellular permeability, such cell lines exhibited a normal overall morphology and formed fully assembled TJs as determined by measuring transepithelial resistance and by immunofluorescence and freeze-fracture analysis. These data indicate that GEF-H1/Lfc is a component of TJs and functions in the regulation of epithelial permeability.

Actin Cytoskeleton↗
PubMed2001

Aniridia-associated translocations, DNase hypersensitivity, sequence comparison and transgenic analysis redefine the functional domain of PAX6.

The transcription factor PAX6 plays a critical, evolutionarily conserved role in eye, brain and olfactory development. Homozygous loss of PAX6 function affects all expressing tissues and is neonatally lethal; heterozygous null mutations cause aniridia in humans and the Small eye (Sey) phenotype in mice. Several upstream and intragenic PAX6 control elements have been defined, generally through transgenesis. However, aniridia cases with chromosomal rearrangements far downstream of an intact PAX6 gene suggested a requirement for additional cis-acting control for correct gene expression. The likely location of such elements is pinpointed through YAC transgenic studies. A 420 kb yeast artificial chromosome (YAC) clone, extending well beyond the most distant patient breakpoint, was previously shown to rescue homozygous Small eye lethality and correct the heterozygous eye phenotype. We now show that a 310 kb YAC clone, terminating just 5' of the breakpoint, fails to influence the Sey phenotypes. Using evolutionary sequence comparison, DNaseI hypersensitivity analysis and transgenic reporter studies, we have identified a region, >150 kb distal to the major PAX6 promoter P1, containing regulatory elements. Components of this downstream regulatory region drive reporter expression in distinct partial PAX6 patterns, indicating that the functional PAX6 gene domain extends far beyond the transcription unit.

Animals↗
PubMed2005

Ecological characterization of the aquatic habitats of mosquitoes (Diptera: Culicidae) in enzootic foci of Venezuelan equine encephalitis virus in western Venezuela.

We studied the aquatic mosquito habitats in and around enzootic foci of Venezuelan Equine Encephalitis virus (VEE) in western Venezuela. Specimens were sampled for 5 mo in three types of vegetation: tall lowland tropical forests, short inundated/secondary growth forests, and pastures/herbaceous vegetation around forests. Ground pools, flooded pastures, swamps, ponds, and canals predominated. We used a multivariate statistical approach to quantitatively assess the relationships of mosquito species with broad categories of the landscape, and with environmental variables within each aquatic habitat. Twenty-four mosquito species in the genera Aedes, Psorophora, Culex, Mansonia, and Uranotaenia were collected. Species richness was higher in the tall forests than in other types of vegetation. Discriminant Function Analysis showed a strong association between landscape category and mosquito species assemblage and identified Culex erraticus Dyar & Knab and Mansonia titillans Walker as indicator species of open areas, and Aedes serratus Theobald as an indicator of tall forests. M. titillans, Uranotaenia geometrica Theobald, Cx. erraticus, and Culex dunni Dyar were associated with unshaded, warm, vegetated waters in flooded pastures and swamps, whereas Ae. serratus, Aedes fulvus (Wiedemann), Psorophora albipes Theobald, Psorophora ferox (Humboldt), Culex caudelli Dyar & Knab, and Culex pedroi Sirivanakarn & Belkin were associated with small, shaded ground pools within the tall forests. Culex coronator Dyar & Knab was associated with partially exposed sites within short forests. These results allowed us to interpret better our previous studies on mosquito adult spread in the study area and their possible role as VEEV disseminators.

Animals↗
PubMed2002

Skin colour and skin cancer - MC1R, the genetic link.

Pigmentary traits such as red hair, fair skin, lack of tanning ability and propensity to freckle (the RHC phenotype) have been identified as genetic risk factors for both melanoma and non-melanocytic skin cancers when combined with the environmental risk factor of high ultraviolet light exposure. The human melanocortin-1 receptor (MC1R) is a key determinant of the pigmentation process and can account in large part for the diverse range of variation in human pigmentation phenotypes and skin phototypes. The coding sequence is highly polymorphic in human populations, with several of these variant forms of the receptor now known to be associated with the RHC phenotype. We have examined variant allele frequencies in the general population and in a collection of adolescent dizygotic and monozygotic twins with defined pigmentation characteristics. Variant allele frequencies have also been determined in several case-control studies of sporadic melanoma, basal cell carcinoma and squamous cell carcinoma, and in familial melanoma kindreds collected within Australia. These studies have shown that three RHC alleles - Arg151Cys, Arg160Trp and Asp294His - were associated with increased risk in all forms of skin cancer and with penetrance and age of onset in familial melanoma in mutation carriers. There is a significant RHC allele heterozygote carrier effect on skin phototype and skin cancer risk, which indicates that variant alleles do not behave in a strictly recessive manner. Ultimately, the genetic and chemical assessment of melanin synthesis rather than skin colour will be the best indicator for skin cancer risk, and such genetic association studies combined with functional analysis of variant alleles should provide the link to understanding skin phototypes.

Alleles↗
PubMed1991

Functional epitope analysis of the human CD11a/CD18 molecule (LFA-1, lymphocyte function-associated antigen 1) involved in HIV-1-induced syncytium formation.

After binding to the CD4 receptor, the human immunodeficiency virus 1 (HIV-1) may enter the T cell and induce the formation of multinucleated giant cells (syncytia). As well as the CD4 molecule, other molecules, such as the lymphocyte function-associated antigen 1 (LFA-1, CD11a/CD18) have been shown to be involved in HIV-1-mediated cell fusion. This study was designed to define regions on the human CD11a/CD18 molecule important for the HIV-1-induced syncytium formation. A CD11a/CD18 MoAb panel discriminating at least five distinct and spatially distant domains on the LFA-1 molecule was used. Comparison of the functional activity of different MoAbs demonstrated that all epitopes of the LFA-1 molecule were not of equal importance in HIV-1-induced syncytium formation between H9.III cells chronically infected with HIV-1 and uninfected CD4+ SupT1 cells. We also demonstrated that CD11a/CD18 MoAbs inhibit syncytia formation only at the level of the uninfected SupT1 cells, suggesting that the LFA-1 molecule expressed on SupT1 cells interacts with ligand(s) expressed on the infected H9.III cells. Two potential LFA-1 receptors on the H9.III cells were tested: the ICAM-1 molecule (intercellular adhesion molecule 1, CD54) and the HIV-1 transmembrane glycoprotein 41 (gp41). A CD54 MoAb (84H10) partially inhibited syncytia formation, thus demonstrating the involvement of the ICAM-1 molecule in the HIV-1-mediated cell fusion. However, the CD11a/CD18 MoAbs do not inhibit binding of the viral envelope glycoprotein gp41 to the cell surface, irrespective of the MoAb concentration used. Although we have not been successful in identifying all candidate fusion receptors for the LFA-1 molecule, these data suggest that some LFA-1 regions are important for syncytium formation and, therefore, in the cell-to-cell transmission of virus and in the spread of infection.

Acquired Immunodeficiency Syndrome↗
PubMed2001

Nef enhances human immunodeficiency virus type 1 infectivity resulting from intervirion fusion: evidence supporting a role for Nef at the virion envelope.

The human immunodeficiency virus type 1 (HIV-1) accessory protein Nef stimulates viral infectivity by facilitating an early event in the HIV-1 life cycle. Although no structural or biochemical defects in Nef-defective HIV-1 particles have been demonstrated, the Nef protein is incorporated into HIV-1 particles. To localize the function of Nef within the virus particle, we developed a novel technology involving fusion of enveloped donor HIV-1 particles bearing core defects with envelope-defective target virions bearing HIV-1 receptors. Although neither virus alone was capable of infecting CD4(+) target cells, the incubation of donor and target virions prior to addition to target cells resulted in infection. This effect, termed "virion transcomplementation," required a functional Env protein on the donor virus and CD4 and an appropriate coreceptor on target virions. To provide evidence for intervirion fusion as the mechanism of complementation, experiments were performed using dual-enveloped HIV-1 particles bearing both HIV-1 and ecotropic murine leukemia virus (E-MLV) Env proteins as donor virions. Infection of CD4-negative target cells bearing E-MLV receptors was prevented by HIV-1 entry inhibitors when added before, but not after, incubation of donor and target virions prior to the addition to cells. When we used Nef(+) and Nef(-) donor and target virions, Nef enhanced infection when present in donor virions. In contrast, no effect of Nef was detected when present in the target virus. These results reveal a potential mechanism for enhancing HIV-1 diversity in vivo through the rescue of defective viral genomes and provide a novel genetic system for the functional analysis of virion-associated proteins in HIV-1 infection.

CD4-Positive T-Lymphocytes↗
PubMed2001

Modulation of different human immunodeficiency virus type 1 Nef functions during progression to AIDS.

The human immunodeficiency virus type 1 (HIV-1) Nef protein has several independent functions that might contribute to efficient viral replication in vivo. Since HIV-1 adapts rapidly to its host environment, we investigated if different Nef properties are associated with disease progression. Functional analysis revealed that nef alleles obtained during late stages of infection did not efficiently downmodulate class I major histocompatibility complex but were highly active in the stimulation of viral replication. In comparison, functional activity in downregulation of CD4 and enhancement of HIV-1 infectivity were maintained or enhanced after AIDS progression. Our results demonstrate that various Nef activities are modulated during the course of HIV-1 infection to maintain high viral loads at different stages of disease progression. These findings suggest that all in vitro Nef functions investigated contribute to AIDS pathogenesis and indicate that nef variants with increased pathogenicity emerge in a significant number of HIV-1-infected individuals.

Acquired Immunodeficiency Syndrome↗
PubMed2006

Alterations in cerebral dynamics at high altitude following partial acclimatization in humans: wakefulness and sleep.

We tested the hypothesis that, following exposure to high altitude, cerebrovascular reactivity to CO2 and cerebral autoregulation would be attenuated. Such alterations may predispose to central sleep apnea at high altitude by promoting changes in brain PCO2 and thus breathing stability. We measured middle cerebral artery blood flow velocity (MCAv; transcranial Doppler ultrasound) and arterial blood pressure during wakefulness in conditions of eucapnia (room air), hypocapnia (voluntary hyperventilation), and hypercapnia (isooxic rebeathing), and also during non-rapid eye movement (stage 2) sleep at low altitude (1,400 m) and at high altitude (3,840 m) in five individuals. At each altitude, sleep was studied using full polysomnography, and resting arterial blood gases were obtained. During wakefulness and polysomnographic-monitored sleep, dynamic cerebral autoregulation and steady-state changes in MCAv in relation to changes in blood pressure were evaluated using transfer function analysis. High altitude was associated with an increase in central sleep apnea index (0.2 +/- 0.4 to 20.7 +/- 23.2 per hour) and an increase in mean blood pressure and cerebrovascular resistance during wakefulness and sleep. MCAv was unchanged during wakefulness, whereas there was a greater decrease during sleep at high altitude compared with low altitude (-9.1 +/- 1.7 vs. -4.8 +/- 0.7 cm/s; P < 0.05). At high altitude, compared with low altitude, the cerebrovascular reactivity to CO2 in the hypercapnic range was unchanged (5.5 +/- 0.7 vs. 5.3 +/- 0.7%/mmHg; P = 0.06), while it was lowered in the hypocapnic range (3.1 +/- 0.7 vs. 1.9 +/- 0.6%/mmHg; P < 0.05). Dynamic cerebral autoregulation was further reduced during sleep (P < 0.05 vs. low altitude). Lowered cerebrovascular reactivity to CO2 and reduction in both dynamic cerebral autoregulation and MCAv during sleep at high altitude may be factors in the pathogenesis of breathing instability.

Acclimatization↗
PubMed2005

Phydbac "Gene Function Predictor": a gene annotation tool based on genomic context analysis.

BACKGROUND: The large amount of completely sequenced genomes allows genomic context analysis to predict reliable functional associations between prokaryotic proteins. Major methods rely on the fact that genes encoding physically interacting partners or members of shared metabolic pathways tend to be proximate on the genome, to evolve in a correlated manner and to be fused as a single sequence in another organism. RESULTS: The new "Gene Function Predictor", linked to the web server Phydbac proposes putative associations between Escherichia coli K-12 proteins derived from a combination of these methods. We show that associations made by this tool are more accurate than linkages found in the other established databases. Predicted assignments to GO categories, based on pre-existing functional annotations of associated proteins are also available. This new database currently holds 9,379 pairwise links at an expected success rate of at least 80%, the 6,466 functional predictions to GO terms derived from these links having a level of accuracy higher than 70%. CONCLUSION: The "Gene Function Predictor" is an automatic tool that aims to help biologists by providing them hypothetical functional predictions out of genomic context characteristics. The "Gene Function predictor" is available at http://www.igs.cnrs-mrs.fr/phydbac/indexPS.html.

Algorithms↗
PubMed2004

High-resolution mapping and functional analysis of se2.1: a major stigma exsertion quantitative trait locus associated with the evolution from allogamy to autogamy in the genus Lycopersicon.

The degree to which stigmas are exserted above the stamen in flowers is a key determinant of cross-pollination (and hence allogamy) in many plant species. Most species in the genus Lycopersicon are obligate or facultative outcrossers and bear flowers with highly exserted stigmas. In contrast, the cultivated tomato (Lycopersicon esculentum) bears flowers with flush or inserted stigmas promoting self-fertilization. It has been observed that a major QTL, se2.1, on chromosome 2 is responsible for a large portion of phenotypic variation for this trait and that mutation(s) at this locus were likely involved in the evolution from allogamy to autogamy in this genus. To understand the genetic and molecular basis of stigma exsertion, we have conducted a high-resolution mapping at the chromosome region harboring the se2.1 QTL. The results indicate that this is a compound locus, comprising at least five tightly linked genes, one controlling style length, three controlling stamen length, and the other affecting anther dehiscence, a taxonomic character used to distinguish Lycopersicon species from other solanaceous species. This cluster of genes may represent the vestiges of an ancient coadapted gene complex in controlling mating behavior.

Alleles↗
PubMed1981

An introduction to the coherence function and its use in EEG signal analysis.

The coherence function quantifies the association between pairs of signals as a function of frequency and has been shown to be useful for measuring changes in EEG topography related to cognitive tasks, psychopathology, and other aspects of brain organisation. For a narrow frequency band, its magnitude is analogous to the correlation coefficient between the signals limited by that band, but its value may differ because of the way that smoothing over frequency is achieved. The coherence function is described in physical terms using simple waveforms.

Brain↗
PubMed1993

Behavioural techniques to reduce self-injurious behaviour in children with autism.

This paper is part of a special section on 'self-injurious behaviour and autism' and concentrates on behavioural treatment techniques available and useful to reduce self-injurious behaviour in children with autism (e.g. extinction, time-out, differential reinforcement, alternative forms of stimulation, sensory deprivation, physical restraint, crisis management, environmental modifications). It has become increasingly evident that the successful treatment of self-injurious behaviour requires, first, a systematic and detailed (functional) analysis of the variables associated with the behaviour and, second, a hypothesis-testing approach on an individual, naturalistic basis to increase the acquisition of alternative skills and self-control.

Autistic Disorder↗
PubMed2001

Structural and functional genomics in domestic animals: the way to understand the phenotype.

Molecular approaches to genome analysis in livestock are reviewed by discussing the contribution of molecular genome analysis to the identification of the genetic variation underlying phenotypic variation (structural genome analysis) and to the definition of the trait-associated and environment-affected gene expression (functional genome analysis) as an important prerequisite to understanding the formation of a phenotype. Aspects of using mapped 'quantitative trait loci' (QTL) or gene variants as well as the identified trait-associated and environment-affected gene expression profile in livestock production are expounded.

Journal Article↗
PubMed1995

Functional domain analysis of interferon consensus sequence binding protein (ICSBP) and its association with interferon regulatory factors.

Interferon consensus sequence binding protein (ICSBP) is a member of the interferon regulatory factor (IRF) family of proteins that include IRF-1, IRF-2, and ISGF3gamma which share sequence similarity at the putative DNA binding domain (DBD). ICSBP is expressed exclusively in cells of the immune system and acts as a repressor of interferon consensus sequence (ICS) containing promoters that can be alleviated by interferons. In this communication, we have searched for functional domains of ICSBP by dissecting the DBD from the repression activity. The putative DBD of ICSBP (amino acids 1-121) when fused in frame to the transcriptional activation domain of the herpes simplex VP16 (ICSBP-VP16) is a very strong activator of ICS-containing promoters. In addition, ICSBP-VP16 fusion construct transfected into adenovirus (Ad) 12 transformed cells enabled cell surface expression of major histocompatibility complex class I antigens as did treatment with interferon. On the other hand, the DBD of the yeast transcriptional activator GAL4 was fused in frame to a truncated ICSBP in which the DBD was impaired resulting in a chimeric construct GAL4-ICSBP. This construct is capable of repressing promoters containing GAL4 binding sites. Thus, ICSBP contains at least two independent domains: a DBD and a transcriptional repressor domain. Furthermore, we have tested possible interactions between ICSBP and IRFs. The chimeric construct GAL4-ICSBP inhibited the stimulated effect of IRF-1 on a reporter gene, implying for a possible interaction between IRF-1 and ICSBP. Electromobility shift assays, demonstrated that ICSBP can associate with IRF-2 or IRF-1 in vitro as well as in vivo. Thus, ICSBP contains a third functional domain that enables the association with IRFs. These associations are probably important for the fine balance between positive and negative regulators involved in the interferon-mediated signal transduction pathways in cells of the immune system.

Base Sequence↗