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Search Results: 1 - 10 of 402332 matches for " Hugh M. Robertson "
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The Caenorhabditis chemoreceptor gene families
James H Thomas, Hugh M Robertson
BMC Biology , 2008, DOI: 10.1186/1741-7007-6-42
Abstract: Based on manual curation and sequence comparisons among putative G-protein-coupled chemoreceptor genes in the nematode Caenorhabditis elegans, we identified approximately 1300 genes and 400 pseudogenes in the 19 largest gene families, most of which fall into larger superfamilies. In the related species C. briggsae and C. remanei, we identified most or all genes in each of the 19 families. For most families, C. elegans has the largest number of genes and C. briggsae the smallest number, suggesting changes in the importance of chemoperception among the species. Protein trees reveal family-specific and species-specific patterns of gene duplication and gene loss. The frequency of strict orthologs varies among the families, from just over 50% in two families to less than 5% in three families. Several families include large species-specific expansions, mostly in C. elegans and C. remanei.Chemoreceptor gene families in Caenorhabditis species are large and evolutionarily dynamic as a result of gene duplication and gene loss. These dynamics shape the chemoreceptor gene complements in Caenorhabditis species and define the receptor space available for chemosensory responses. To explain these patterns, we propose the gray pawn hypothesis: individual genes are of little significance, but the aggregate of a large number of diverse genes is required to cover a large phenotype space.Chemoperception is a central sense in nematodes, which lack vision and hearing. Detailed analysis of the cellular basis of chemosensory responses in Caenorhabditis elegans has shown that a small number of sensory neurons mediate all known responses [1]. Despite this cellular simplicity, a huge number of genes encode candidate receptors for chemical stimuli. The first indication of these genes came from an analysis of the partially completed genome sequence in 1995. This work identified several small genomic clusters of related genes encoding members of the rhodopsin superfamily of G-protein-coupled rece
Evolution of the sugar receptors in insects
Lauren B Kent, Hugh M Robertson
BMC Evolutionary Biology , 2009, DOI: 10.1186/1471-2148-9-41
Abstract: While most Drosophila species retain all eight genes, we find that the three Drosophila subgenus species have lost Gr64d, while D. grimshawi and the D. pseudoobscura/persimilis sibling species have also lost Gr5a function. The entire Gr64 gene complex was also duplicated in the D. grimshawi lineage, but only one potentially functional copy of each gene has been retained. The numbers of SRs range from two in the hymenopterans Apis mellifera and Nasonia vitripennis to 16 in the beetle Tribolium castaneum. An unusual aspect is the evolution of a novel exon from intronic sequence in an expanded set of four SRs in Bombyx mori (BmGr5-8), which appears to be the first example of such exonization in insects. Twelve intron gains and 63 losses are inferred within the SR family.Examination of the SRs in these fly, mosquito, moth, beetle, and hymenopteran genome sequences reveals that they appear to have originated independently from single ancestral genes within the dipteran and coleopteran lineages, and two genes in the lepidopteran and hymenopteran lineages. The origin of the insect SRs will eventually be illuminated by additional basal insect and arthropod genome sequences.Sugars serve as some of the simplest, most easily metabolized forms of energy available to life. For example, despite an anautogenous female mosquito's need for a bloodmeal to nourish her developing eggs, it is the simple nectar of plants that fuels her flight muscles and daily energy needs. As sugar is a valuable resource, it seems fitting that most animals have the ability to taste sugars, and in many it forms a primary stimulatory signal for feeding. The molecular basis for sugar detection in insects has been revealed in Drosophila melanogaster where it involves a series of at least eight genes in the gustatory receptor (Gr) family [1-3]. The first of these is Gr5a on the X chromosome, although identification of this gene as encoding a trehalose receptor was initially confused with the neighboring Tre
Odorant Binding Proteins of the Red Imported Fire Ant, Solenopsis invicta: An Example of the Problems Facing the Analysis of Widely Divergent Proteins
Dietrich Gotzek,Hugh M. Robertson,Yannick Wurm,DeWayne Shoemaker
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0016289
Abstract: We describe the odorant binding proteins (OBPs) of the red imported fire ant, Solenopsis invicta, obtained from analyses of an EST library and separate 454 sequencing runs of two normalized cDNA libraries. We identified a total of 18 putative functional OBPs in this ant. A third of the fire ant OBPs are orthologs to honey bee OBPs. Another third of the OBPs belong to a lineage-specific expansion, which is a common feature of insect OBP evolution. Like other OBPs, the different fire ant OBPs share little sequence similarity (~20%), rendering evolutionary analyses difficult. We discuss the resulting problems with sequence alignment, phylogenetic analysis, and tests of selection. As previously suggested, our results underscore the importance for careful exploration of the sensitivity to the effects of alignment methods for data comprising widely divergent sequences.
The chemoreceptor genes of the waterflea Daphnia pulex: many Grs but no Ors
D Carolina Pe?alva-Arana, Michael Lynch, Hugh M Robertson
BMC Evolutionary Biology , 2009, DOI: 10.1186/1471-2148-9-79
Abstract: We describe 58 Grs (gustatory receptors), belonging to the insect chemoreceptor superfamily, which were identified bioinformatically in the draft genome of the crustacean waterflea Daphnia pulex. No genes encoding proteins similar to the insect odorant receptors (Ors) were identified. These 58 Grs form 3 distinctive subfamilies of 37, 12, and 5 genes, as well as a highly divergent singleton (Gr58). In addition, Grs55–57 share distinctive amino acid motifs and cluster with the sugar receptors of insects, and may illuminate the origin of this distinctive subfamily. ESTs, tiling array, and PCR amplification results support 34 predicted gene models, and preliminary expression data comparing the sexes indicates potential female-biased expression for some genes.This repertoire of 58 chemoreceptors presumably mediates the many chemoperception abilities of waterfleas. While it is always possible that the entire Or gene lineage was lost at some point in the history of Daphnia pulex, we think it more likely that the insect Or lineage is indeed a relatively recently expanded gene lineage concomitant with the evolution of terrestriality in the insects or their hexapod ancestors.The ability of Daphnia to detect chemical cues released by prey or predator have been glimpsed through studies on feeding behavior and predator avoidance [1,2]. Daphnids reject food particles, adjust feeding currents according to food availability, quality and surrounding chemical cues, and appear to swim and remain in areas where food is abundant [3-6]. However, their presence in food abundant areas can be altered by the presence of predators, and their vertical distribution is often associated with the presence or absence of predators [6,7].Kairomones from predators, fish or invertebrate, affect Daphnia's swimming patterns, dial vertical migration, and even affect morphology [2,8-11]. Species of Daphnia can develop neck teeth, thicker carapaces, and/or long head spines to reduce their vulnerability to
A new member of the GM130 golgin subfamily is expressed in the optic lobe anlagen of the metamorphosing brain of Manduca sexta
Chiou-Miin Wang,Chun-Liang Chen,Hugh M. Robertson,Susan E. Fahrbach
Journal of Insect Science , 2003,
Abstract: During metamorphosis of the insect brain, the optic lobe anlagen generate the proliferation centers for the visual cortices. We show here that, in the moth Manduca sexta, an 80 kDa Golgi complex protein (Ms-golgin80) is abundantly expressed in the cytoplasm of neuroblasts and ganglion mother cells in the optic lobe anlagen and proliferation centers. The predicted amino acid sequence for Ms-golgin80 is similar to that of several members of the GM130 subfamily of Golgi-associated proteins, including rat GM130 and human golgin-95. Homologs of Ms-golgin80 from Drosophila melanogaster, Caenorhabditis elegans, and Brugia malayi were identified through homology sequence search. Sequence similarities are present in three regions: the N-terminus, an internal domain of 89 amino acids, and another domain of 89 amino acids near the C-terminus. Structural similarities further suggest that these molecules play the same cellular role as GM130. GM130 is involved in the docking and fusion of coatomer (COP I) coated vesicles to the Golgi membranes; it also regulates the fragmentation and subsequent reassembly of the Golgi complex during mitosis. Abundant expression of Ms-golgin80 in neuroblasts and ganglion mother cells and its reduced expression in the neuronal progeny of these cells suggest that this protein may be involved in the maintenance of the proliferative state.
Widespread Genome Reorganization of an Obligate Virus Mutualist
Gaelen R. Burke ,Kimberly K. O. Walden,James B. Whitfield,Hugh M. Robertson,Michael R. Strand
PLOS Genetics , 2014, DOI: doi/10.1371/journal.pgen.1004660
Abstract: The family Polydnaviridae is of interest because it provides the best example of viruses that have evolved a mutualistic association with their animal hosts. Polydnaviruses in the genus Bracovirus are strictly associated with parasitoid wasps in the family Braconidae, and evolved ~100 million years ago from a nudivirus. Each wasp species relies on its associated bracovirus to parasitize hosts, while each bracovirus relies on its wasp for vertical transmission. Prior studies establish that bracovirus genomes consist of proviral segments and nudivirus-like replication genes, but how these components are organized in the genomes of wasps is unknown. Here, we sequenced the genome of the wasp Microplitis demolitor to characterize the proviral genome of M. demolitor bracovirus (MdBV). Unlike nudiviruses, bracoviruses produce virions that package multiple circular, double-stranded DNAs. DNA segments packaged into MdBV virions resided in eight dispersed loci in the M. demolitor genome. Each proviral segment was bounded by homologous motifs that guide processing to form mature viral DNAs. Rapid evolution of proviral segments obscured homology between other bracovirus-carrying wasps and MdBV. However, some domains flanking MdBV proviral loci were shared with other species. All MdBV genes previously identified to encode proteins required for replication were identified. Some of these genes resided in a multigene cluster but others, including subunits of the RNA polymerase that transcribes structural genes and integrases that process proviral segments, were widely dispersed in the M. demolitor genome. Overall, our results indicate that genome dispersal is a key feature in the evolution of bracoviruses into mutualists.
Odorant and Gustatory Receptors in the Tsetse Fly Glossina morsitans morsitans
George F. O. Obiero,Paul O. Mireji,Steven R. G. Nyanjom,Alan Christoffels,Hugh M. Robertson,Daniel K. Masiga
PLOS Neglected Tropical Diseases , 2014, DOI: 10.1371/journal.pntd.0002663
Abstract: Tsetse flies use olfactory and gustatory responses, through odorant and gustatory receptors (ORs and GRs), to interact with their environment. Glossina morsitans morsitans genome ORs and GRs were annotated using homologs of these genes in Drosophila melanogaster and an ab initio approach based on OR and GR specific motifs in G. m. morsitans gene models coupled to gene ontology (GO). Phylogenetic relationships among the ORs or GRs and the homologs were determined using Maximum Likelihood estimates. Relative expression levels among the G. m. morsitans ORs or GRs were established using RNA-seq data derived from adult female fly. Overall, 46 and 14 putative G. m. morsitans ORs and GRs respectively were recovered. These were reduced by 12 and 59 ORs and GRs respectively compared to D. melanogaster. Six of the ORs were homologous to a single D. melanogaster OR (DmOr67d) associated with mating deterrence in females. Sweet taste GRs, present in all the other Diptera, were not recovered in G. m. morsitans. The GRs associated with detection of CO2 were conserved in G. m. morsitans relative to D. melanogaster. RNA-sequence data analysis revealed expression of GmmOR15 locus represented over 90% of expression profiles for the ORs. The G. m. morsitans ORs or GRs were phylogenetically closer to those in D. melanogaster than to other insects assessed. We found the chemoreceptor repertoire in G. m. morsitans smaller than other Diptera, and we postulate that this may be related to the restricted diet of blood-meal for both sexes of tsetse flies. However, the clade of some specific receptors has been expanded, indicative of their potential importance in chemoreception in the tsetse.
Genetic Structure of Avian Influenza Viruses from Ducks of the Atlantic Flyway of North America
Yanyan Huang, Michelle Wille, Ashley Dobbin, Natasha M. Walzth?ni, Gregory J. Robertson, Davor Ojkic, Hugh Whitney, Andrew S. Lang
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0086999
Abstract: Wild birds, including waterfowl such as ducks, are reservoir hosts of influenza A viruses. Despite the increased number of avian influenza virus (AIV) genome sequences available, our understanding of AIV genetic structure and transmission through space and time in waterfowl in North America is still limited. In particular, AIVs in ducks of the Atlantic flyway of North America have not been thoroughly investigated. To begin to address this gap, we analyzed 109 AIV genome sequences from ducks in the Atlantic flyway to determine their genetic structure and to document the extent of gene flow in the context of sequences from other locations and other avian and mammalian host groups. The analyses included 25 AIVs from ducks from Newfoundland, Canada, from 2008–2011 and 84 available reference duck AIVs from the Atlantic flyway from 2006–2011. A vast diversity of viral genes and genomes was identified in the 109 viruses. The genetic structure differed amongst the 8 viral segments with predominant single lineages found for the PB2, PB1 and M segments, increased diversity found for the PA, NP and NS segments (2, 3 and 3 lineages, respectively), and the highest diversity found for the HA and NA segments (12 and 9 lineages, respectively). Identification of inter-hemispheric transmissions was rare with only 2% of the genes of Eurasian origin. Virus transmission between ducks and other bird groups was investigated, with 57.3% of the genes having highly similar (≥99% nucleotide identity) genes detected in birds other than ducks. Transmission between North American flyways has been frequent and 75.8% of the genes were highly similar to genes found in other North American flyways. However, the duck AIV genes did display spatial distribution bias, which was demonstrated by the different population sizes of specific viral genes in one or two neighbouring flyways compared to more distant flyways.
Functional Characterization of Transcription Factor Motifs Using Cross-species Comparison across Large Evolutionary Distances
Jaebum Kim,Ryan Cunningham,Brian James,Stefan Wyder,Joshua D. Gibson,Oliver Niehuis,Evgeny M. Zdobnov,Hugh M. Robertson,Gene E. Robinson,John H. Werren,Saurabh Sinha
PLOS Computational Biology , 2010, DOI: 10.1371/journal.pcbi.1000652
Abstract: We address the problem of finding statistically significant associations between cis-regulatory motifs and functional gene sets, in order to understand the biological roles of transcription factors. We develop a computational framework for this task, whose features include a new statistical score for motif scanning, the use of different scores for predicting targets of different motifs, and new ways to deal with redundancies among significant motif–function associations. This framework is applied to the recently sequenced genome of the jewel wasp, Nasonia vitripennis, making use of the existing knowledge of motifs and gene annotations in another insect genome, that of the fruitfly. The framework uses cross-species comparison to improve the specificity of its predictions, and does so without relying upon non-coding sequence alignment. It is therefore well suited for comparative genomics across large evolutionary divergences, where existing alignment-based methods are not applicable. We also apply the framework to find motifs associated with socially regulated gene sets in the honeybee, Apis mellifera, using comparisons with Nasonia, a solitary species, to identify honeybee-specific associations.
Conserved Alternative Splicing and Expression Patterns of Arthropod N-Cadherin
Shu-Ning Hsu ,Shinichi Yonekura,Chun-Yuan Ting,Hugh M. Robertson,Youichi Iwai,Tadashi Uemura,Chi-Hon Lee,Akira Chiba
PLOS Genetics , 2009, DOI: 10.1371/journal.pgen.1000441
Abstract: Metazoan development requires complex mechanisms to generate cells with diverse function. Alternative splicing of pre-mRNA not only expands proteomic diversity but also provides a means to regulate tissue-specific molecular expression. The N-Cadherin gene in Drosophila contains three pairs of mutually-exclusive alternatively-spliced exons (MEs). However, no significant differences among the resulting protein isoforms have been successfully demonstrated in vivo. Furthermore, while the N-Cadherin gene products exhibit a complex spatiotemporal expression pattern within embryos, its underlying mechanisms and significance remain unknown. Here, we present results that suggest a critical role for alternative splicing in producing a crucial and reproducible complexity in the expression pattern of arthropod N-Cadherin. We demonstrate that the arthropod N-Cadherin gene has maintained the three sets of MEs for over 400 million years using in silico and in vivo approaches. Expression of isoforms derived from these MEs receives precise spatiotemporal control critical during development. Both Drosophila and Tribolium use ME-13a and ME-13b in “neural” and “mesodermal” splice variants, respectively. As proteins, either ME-13a- or ME-13b-containing isoform can cell-autonomously rescue the embryonic lethality caused by genetic loss of N-Cadherin. Ectopic muscle expression of either isoform beyond the time it normally ceases leads to paralysis and lethality. Together, our results offer an example of well-conserved alternative splicing increasing cellular diversity in metazoans.
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