CLOE: Identification of Putative Functional Relationships Among Genes by Comparison of Expression Profiles Between Two Species

BMC Bioinformatics. Nov, 2004  |  Pubmed ID: 15550177

Public repositories of microarray data contain an incredible amount of information that is potentially relevant to explore functional relationships among genes by meta-analysis of expression profiles. However, the widespread use of this resource by the scientific community is at the moment limited by the limited availability of effective tools of analysis. We here describe CLOE, a simple cDNA microarray data mining strategy based on meta-analysis of datasets from pairs of species. The method consists in ranking EST probes in the datasets of the two species according to the similarity of their expression profiles with that of two EST probes from orthologous genes, and extracting orthologous EST pairs from a given top interval of the ranked lists. The Gene Ontology annotation of the obtained candidate partners is then analyzed for keywords overrepresentation.

Harshlight: a "corrective Make-up" Program for Microarray Chips

BMC Bioinformatics. 2005  |  Pubmed ID: 16336691

Microscopists are familiar with many blemishes that fluorescence images can have due to dust and debris, glass flaws, uneven distribution of fluids or surface coatings, etc. Microarray scans do show similar artifacts, which might affect subsequent analysis. Although all but the starkest blemishes are hard to find by the unaided eye, particularly in high-density oligonucleotide arrays (HDONAs), few tools are available to help with the detection of those defects.

Microarray and Large-scale in Silico--based Identification of Genes Functionally Related to Haptoglobin And/or Hemopexin

DNA and Cell Biology. Jun, 2006  |  Pubmed ID: 16792502

Haptoglobin and Hemopexin are plasma acute phase proteins that bind with high-affinity hemoglobin and heme, respectively. They play a key role in the protection against oxidative stress and inflammation. To dissect in more detail the mechanism of action of Haptoglobin and Hemopexin, it is important to identify their downstream effectors as well as genes functionally related to them. To this end, we performed a cDNA microarray analysis to compare gene expression profiles of the liver of Haptoglobin and Hemopexin single and double null mice to that of wild-type controls. Then, to extract the best candidates considered to be functionally related to Haptoglobin and/or Hemopexin from microarray-derived gene lists, we used a bioinformatic approach consisting in the screening of published microarray data for genes showing coexpression with Haptoglobin or Hemopexin. This strategy allowed us to identify a group of genes coexpressed with Haptoglobin or Hemopexin and transcriptionally modulated by their lack. These genes present a high probability to be functionally related to Haptoglobin and Hemopexin. Based on literature data, we picked up from this group of genes the ras suppressor Rsu1, the member of the G-protein signal transduction family Gnai2, and the cytokine Mdk as the best candidates mediating the anti-inflammatory action of Haptoglobin and Hemopexin.

Bioinformatics Tools Enabling U-statistics for Microarrays

Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference. 2006  |  Pubmed ID: 17947031

It is rare that a single gene is sufficient to represent all aspects of genomic activity. Similarly, most common diseases cannot be explained by a mutations at a single locus. Since complex systems tend to be neither linear nor hierarchical in nature, but to have correlated components of unknown relative importance, the assumptions of traditional (parametric) multivariate statistical methods can rarely be justified on theoretical grounds. Empirical "validation" is not only problematic, but also time consuming. Here we demonstrates how bioinformatics tools, ranging from spreadsheets to grids, can enable u-statistics as a non-parametric alternative for scoring multivariate ordinal data. Applications are shown to improve assessment of genetic risk factors, quality control of microarrays and signal value estimation, scoring genomic profiles that best correlated with complex risk factors (cardiovascular diseases), and complex responses to an intervention (treatment of psoriasis).

Detecting Artifacts on SNP Chips

Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference. 2006  |  Pubmed ID: 17947067

Microscopists are familiar with many blemishes that fluorescence images can have due to dust and debris, glass flaws, uneven distribution of fluids or surface coatings, etc. Microarray scans do show similar artifacts, which might affect subsequent analysis. We developed a tool, Harshlight, for the detection and masking of blemishes in HDONA microarray chips. Harshlight uses a combination of statistic and image processing methods to identify defects. We demonstrate that Harshlight can be widely used for chips with different technologies thanks to its user-tunable parameters. Here we report its application to SNP microarrays.

The RhoA-associated Protein Citron-N Controls Dendritic Spine Maintenance by Interacting with Spine-associated Golgi Compartments

EMBO Reports. Apr, 2008  |  Pubmed ID: 18309323

Dendritic spines are highly dynamic protuberances that are thought to be crucial for learning and memory. Although it is well known that actin filaments and membrane dynamics regulate spine plasticity, how these two events are linked locally is less clear. Here, we provide evidence that Citron-N (CIT-N), a binding partner of the small GTPase RhoA, is associated with the actin filaments and Golgi compartments of dendritic spines. We also show that CIT-N is required for recruiting F-actin and Golgi membranes at spines of in vitro-grown neurons. Studies in knockout mice show that this protein is essential for the maturation of dendritic spines. We suggest that CIT-N might function as a scaffold protein in spine organization through its ability to bind to Golgi membranes and by affecting actin remodelling.

Insect Odorant Receptors Are Molecular Targets of the Insect Repellent DEET

Science (New York, N.Y.). Mar, 2008  |  Pubmed ID: 18339904

DEET (N,N-diethyl-meta-toluamide) is the world's most widely used topical insect repellent, with broad effectiveness against most insects. Its mechanism of action and molecular target remain unknown. Here, we show that DEET blocks electrophysiological responses of olfactory sensory neurons to attractive odors in Anopheles gambiae and Drosophila melanogaster. DEET inhibits behavioral attraction to food odors in Drosophila, and this inhibition requires the highly conserved olfactory co-receptor OR83b. DEET inhibits odor-evoked currents mediated by the insect odorant receptor complex, comprising a ligand-binding subunit and OR83b. We conclude that DEET masks host odor by inhibiting subsets of heteromeric insect odorant receptors that require the OR83b co-receptor. The identification of candidate molecular targets for the action of DEET may aid in the design of safer and more effective insect repellents.

Insect Olfactory Receptors Are Heteromeric Ligand-gated Ion Channels

Nature. Apr, 2008  |  Pubmed ID: 18408712

In insects, each olfactory sensory neuron expresses between one and three ligand-binding members of the olfactory receptor (OR) gene family, along with the highly conserved and broadly expressed Or83b co-receptor. The functional insect OR consists of a heteromeric complex of unknown stoichiometry but comprising at least one variable odorant-binding subunit and one constant Or83b family subunit. Insect ORs lack homology to G-protein-coupled chemosensory receptors in vertebrates and possess a distinct seven-transmembrane topology with the amino terminus located intracellularly. Here we provide evidence that heteromeric insect ORs comprise a new class of ligand-activated non-selective cation channels. Heterologous cells expressing silkmoth, fruitfly or mosquito heteromeric OR complexes showed extracellular Ca2+ influx and cation-non-selective ion conductance on stimulation with odorant. Odour-evoked OR currents are independent of known G-protein-coupled second messenger pathways. The fast response kinetics and OR-subunit-dependent K+ ion selectivity of the insect OR complex support the hypothesis that the complex between OR and Or83b itself confers channel activity. Direct evidence for odorant-gated channels was obtained by outside-out patch-clamp recording of Xenopus oocyte and HEK293T cell membranes expressing insect OR complexes. The ligand-gated ion channel formed by an insect OR complex seems to be the basis for a unique strategy that insects have acquired to respond to the olfactory environment.

Life on Top-working at the Rockefeller University, New York

New Biotechnology. Apr, 2009  |  Pubmed ID: 19429537

Smelling the Difference: Controversial Ideas in Insect Olfaction

The Journal of Experimental Biology. Jul, 2009  |  Pubmed ID: 19525421

In animals, the sense of smell is often used as a powerful way to attract potential mates, to find food and to explore the environment. Different animals evolved different systems to detect volatile odorants, tuned to the specific needs of each species. Vertebrates and nematodes have been used extensively as models to study the mechanisms of olfaction: the molecular players are olfactory receptors (ORs) expressed in olfactory sensory neurons (OSNs) where they bind to volatile chemicals, acting as the first relay of olfactory processing. These receptors belong to the G protein-coupled receptor (GPCR) superfamily; binding to odorants induces the production and amplification of second messengers, which lead to the depolarization of the neuron. The anatomical features of the insect olfactory circuit are similar to those of mammals, and until recently it was thought that this similarity extended to the ORs, which were originally annotated as GPCRs. Surprisingly, recent evidence shows that insect ORs can act like ligand-gated ion channels, either completely or partially bypassing the amplification steps connected to the activation of G proteins. Although the involvement of G proteins in insect olfactory signal transduction is still under question, this new discovery raises fascinating new questions regarding the function of the sense of smell in insects, its evolution and potential benefits compared with its mammalian counterpart.

A Natural Polymorphism Alters Odour and DEET Sensitivity in an Insect Odorant Receptor

Nature. Oct, 2011  |  Pubmed ID: 21937991

Blood-feeding insects such as mosquitoes are efficient vectors of human infectious diseases because they are strongly attracted by body heat, carbon dioxide and odours produced by their vertebrate hosts. Insect repellents containing DEET (N,N-diethyl-meta-toluamide) are highly effective, but the mechanism by which this chemical wards off biting insects remains controversial despite decades of investigation. DEET seems to act both at close range as a contact chemorepellent, by affecting insect gustatory receptors, and at long range, by affecting the olfactory system. Two opposing mechanisms for the observed behavioural effects of DEET in the gas phase have been proposed: that DEET interferes with the olfactory system to block host odour recognition and that DEET actively repels insects by activating olfactory neurons that elicit avoidance behaviour. Here we show that DEET functions as a modulator of the odour-gated ion channel formed by the insect odorant receptor complex. The functional insect odorant receptor complex consists of a common co-receptor, ORCO (ref. 15) (formerly called OR83B; ref. 16), and one or more variable odorant receptor subunits that confer odour selectivity. DEET acts on this complex to potentiate or inhibit odour-evoked activity or to inhibit odour-evoked suppression of spontaneous activity. This modulation depends on the specific odorant receptor and the concentration and identity of the odour ligand. We identify a single amino-acid polymorphism in the second transmembrane domain of receptor OR59B in a Drosophila melanogaster strain from Brazil that renders OR59B insensitive to inhibition by the odour ligand and modulation by DEET. Our data indicate that natural variation can modify the sensitivity of an odour-specific insect odorant receptor to odour ligands and DEET. Furthermore, they support the hypothesis that DEET acts as a molecular 'confusant' that scrambles the insect odour code, and provide a compelling explanation for the broad-spectrum efficacy of DEET against multiple insect species.

Post-fasting Olfactory, Transcriptional, and Feeding Responses in Drosophila

Physiology & Behavior. Jan, 2012  |  Pubmed ID: 21945372

The sensation of hunger after a period of fasting and of satiety after eating is crucial to behavioral regulation of food intake, but the biological mechanisms regulating these sensations are incompletely understood. We studied the behavioral and physiological adaptations to fasting in the vinegar fly (Drosophila melanogaster). Here we show that both male and female flies increased their rate of food intake transiently in the post-fasted state. Although the basal feeding rate was higher in females than males, the magnitude of the post-fasting feeding response was the same in both sexes. Flies returned to a stable baseline feeding rate within 12 h after return to food for males and 24 h for females. This modulation in feeding was accompanied by a significant increase in the size of the crop organ of the digestive system, suggesting that fasted flies responded both by increasing their food intake and storing reserve food in their crop. Flies demonstrated increased behavioral attraction to an attractive odor when food-deprived. Expression profiling of head, body, and chemosensory tissues by microarray analysis revealed 415 genes regulated by fasting after 24 h and 723 genes after 48 h, with downregulated genes outnumbering upregulated genes in each tissue and fasting time point. These transcriptional changes showed rich temporal dynamics and affected genes across multiple functional gene ontology categories. These observations suggest that a coordinated transcriptional response to internal physiological state may regulate both ingestive behaviors and chemosensory perception of food.