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1.  ME-07INFLUENCE OF REGIONAL MICROENVIROMENT AND ASTROCYTE HETEROGENEITY ON ASTROCYTOMA DEVELOPMENT 
Neuro-Oncology  2014;16(Suppl 5):v121.
The role of the local microenvironment during early astrocytoma development remains elusive. We previously showed that Rb and Pten inactivation and Kras activation (TRP) transforms Gfap+ astrocytes and induces low-grade astrocytoma tumorigenesis throughout the adult brain. To confirm that astrocytes are the cell of origin, we targeted them using an alternative astrocyte-specific promoter, Glast. In the absence of oncogenic mutations, genetic lineage tracing with Glast-CreER; floxed TdTomato mice produced recombination in 8-38% of Gfap/Blbp+ astrocytes in the cortex, diencephalon, brainstem, and olfactory bulb. EdU labeling showed <0.04% proliferated at 7 days. Astrocyte proliferation (EdU+) increased 8-29-fold 3 weeks and TdTomato+ cells increased 3-7-fold by 8 weeks after TRP transformation. Glast;TdTomato+ astrocytes were rare in the brainstem and their transformation produced minimal tumorigenesis. In contrast, hGFAP-CreER uniformly induced recombination in ∼50% of astrocytes in all regions, including the brainstem. Whereas TdTomato+ astrocytes increased 6-11-fold in hGFAP-TRP mice after 8 weeks, Glast-targeted transformation was 1-4 fold lower. Differences in growth rates were most pronounced in the brainstem (P<0.001), but olfactory bulb growth rates were similar (P>0.05). Both CreER driver and brain region significantly affected astrocyte growth rate (ANOVA P < 0.0003). In both models, transformed astrocytes maintained Gfap/Blbp expression, gained expression of the stem cell marker Nestin, and formed increasingly dense perineuronal satellites over time. Ki-67 labeling showed clonal expansion, as hypercellular foci with 11-fold higher proliferation relative to less-cellular areas of tumor developed by 16 weeks. Glast-, but not hGFAP-driven tumors contained dividing, but untransformed (TdTomato;T121−) BLBP+ astrocytes, IBA1+ microglia, and PDGFRα+ oligodendrocyte progenitors (OPC). Proliferating microglia (6-0%) and OPC (18-5%) decreased over time, while dividing, untransformed astrocytes increased (57-85%). These findings support the notion that regional microenvironment and astrocyte heterogeneity contribute to astrocytoma development. The Glast-TRP model may be useful in dissecting the role of regional microenvironment during astrocytoma tumorigenesis.
doi:10.1093/neuonc/nou261.6
PMCID: PMC4218308
2.  Use of Chimeras, Point Mutants, and Molecular Modeling to Map the Antagonist-binding Site of 4,4′,4″,4‴-(Carbonylbis-(imino-5,1,3-benzenetriylbis(carbonylimino)))tetrakisbenzene-1,3-disulfonic Acid (NF449) at P2X1 Receptors for ATP* 
The Journal of Biological Chemistry  2014;290(3):1559-1569.
Background: NF449 is a selective P2X1 receptor antagonist.
Results: Chimeric/mutant P2X1/4 receptors and molecular docking provided models of NF449 binding.
Conclusion: NF449 is coordinated by the core ATP-binding site, the base of the cysteine-rich head, and the dorsal fin region.
Significance: The study provides insight into the selective antagonism of P2X receptors that may aid rational drug design.
P2X receptor subtype-selective antagonists are promising candidates for treatment of a range of pathophysiological conditions. However, in contrast to high resolution structural understanding of agonist action in the receptors, comparatively little is known about the molecular basis of antagonist binding. We have generated chimeras and point mutations in the extracellular ligand-binding loop of the human P2X1 receptor, which is inhibited by NF449, suramin, and pyridoxal-phosphate-6-azophenyl-2,4-disulfonate, with residues from the rat P2X4 receptor, which is insensitive to these antagonists. There was little or no effect on sensitivity to suramin and pyridoxal-phosphate-6-azophenyl-2,4-disulfonate in chimeric P2X1/4 receptors, indicating that a significant number of residues required for binding of these antagonists are present in the P2X4 receptor. Sensitivity to the P2X1 receptor-selective antagonist NF449 was reduced by ∼60- and ∼135-fold in chimeras replacing the cysteine-rich head, and the dorsal fin region below it in the adjacent subunit, respectively. Point mutants identified the importance of four positively charged residues at the base of the cysteine-rich head and two variant residues in the dorsal fin for high affinity NF449 binding. These six residues were used as the starting area for molecular docking. The four best potential NF449-binding poses were then discriminated by correspondence with the mutagenesis data and an additional mutant to validate the binding of one lobe of NF449 within the core conserved ATP-binding pocket and the other lobes coordinated by positive charge on the cysteine-rich head region and residues in the adjacent dorsal fin.
doi:10.1074/jbc.M114.592246
PMCID: PMC4340402  PMID: 25425641
ATP; Electrophysiology; Ion Channel; Mutagenesis; Purinergic Receptor; NF449; P2X Receptor; PPADS; Ligand-gated Ion Channel; Suramin
3.  Cooperativity between MAPK and PI3K signaling activation is required for glioblastoma pathogenesis 
Neuro-Oncology  2013;15(10):1317-1329.
Background
Glioblastoma (GBM) genomes feature recurrent genetic alterations that dysregulate core intracellular signaling pathways, including the G1/S cell cycle checkpoint and the MAPK and PI3K effector arms of receptor tyrosine kinase (RTK) signaling. Elucidation of the phenotypic consequences of activated RTK effectors is required for the design of effective therapeutic and diagnostic strategies.
Methods
Genetically defined, G1/S checkpoint-defective cortical murine astrocytes with constitutively active Kras and/or Pten deletion mutations were used to systematically investigate the individual and combined roles of these 2 RTK signaling effectors in phenotypic hallmarks of glioblastoma pathogenesis, including growth, migration, and invasion in vitro. A novel syngeneic orthotopic allograft model system was used to examine in vivo tumorigenesis.
Results
Constitutively active Kras and/or Pten deletion mutations activated both MAPK and PI3K signaling. Their combination led to maximal growth, migration, and invasion of G1/S-defective astrocytes in vitro and produced progenitor-like transcriptomal profiles that mimic human proneural GBM. Activation of both RTK effector arms was required for in vivo tumorigenesis and produced highly invasive, proneural-like GBM.
Conclusions
These results suggest that cortical astrocytes can be transformed into GBM and that combined dysregulation of MAPK and PI3K signaling revert G1/S-defective astrocytes to a primitive gene expression state. This genetically-defined, immunocompetent model of proneural GBM will be useful for preclinical development of MAPK/PI3K-targeted, subtype-specific therapies.
doi:10.1093/neuonc/not084
PMCID: PMC3779038  PMID: 23814263
astrocytes; genetically engineered mouse; glioblastoma; invasion; Pten
4.  Malaria Protein Kinase CK2 (PfCK2) Shows Novel Mechanisms of Regulation 
PLoS ONE  2014;9(3):e85391.
Casein kinase 2 (protein kinase CK2) is a conserved eukaryotic serine/theronine kinase with multiple substrates and roles in the regulation of cellular processes such as cellular stress, cell proliferation and apoptosis. Here we report a detailed analysis of the Plasmodium falciparum CK2, PfCK2, demonstrating that this kinase, like the mammalian orthologue, is a dual specificity kinase able to phosphorylate at both serine and tyrosine. However, unlike the human orthologue that is auto-phosphorylated on tyrosine within the activation loop, PfCK2 shows no activation loop auto-phosphorylation but rather is auto-phosphorylated at threonine 63 within subdomain I. Phosphorylation at this site in PfCK2 is shown here to regulate the intrinsic kinase activity of PfCK2. Furthermore, we generate an homology model of PfCK2 in complex with the known selective protein kinase CK2 inhibitor, quinalizarin, and in so doing identify key co-ordinating residues in the ATP binding pocket that could aid in designing selective inhibitors to PfCK2.
doi:10.1371/journal.pone.0085391
PMCID: PMC3962329  PMID: 24658579
5.  Molecular Evolution of a Pervasive Natural Amino-Acid Substitution in Drosophila cryptochrome 
PLoS ONE  2014;9(1):e86483.
Genetic variations in circadian clock genes may serve as molecular adaptations, allowing populations to adapt to local environments. Here, we carried out a survey of genetic variation in Drosophila cryptochrome (cry), the fly’s dedicated circadian photoreceptor. An initial screen of 10 European cry alleles revealed substantial variation, including seven non-synonymous changes. The SNP frequency spectra and the excessive linkage disequilibrium in this locus suggested that this variation is maintained by natural selection. We focused on a non-conservative SNP involving a leucine - histidine replacement (L232H) and found that this polymorphism is common, with both alleles at intermediate frequencies across 27 populations surveyed in Europe, irrespective of latitude. Remarkably, we were able to reproduce this natural observation in the laboratory using replicate population cages where the minor allele frequency was initially set to 10%. Within 20 generations, the two allelic variants converged to approximately equal frequencies. Further experiments using congenic strains, showed that this SNP has a phenotypic impact, with variants showing significantly different eclosion profiles. At the long term, these phase differences in eclosion may contribute to genetic differentiation among individuals, and shape the evolution of wild populations.
doi:10.1371/journal.pone.0086483
PMCID: PMC3901690  PMID: 24475129
6.  The splicing landscape is globally reprogrammed during male meiosis 
Nucleic Acids Research  2013;41(22):10170-10184.
Meiosis requires conserved transcriptional changes, but it is not known whether there is a corresponding set of RNA splicing switches. Here, we used RNAseq of mouse testis to identify changes associated with the progression from mitotic spermatogonia to meiotic spermatocytes. We identified ∼150 splicing switches, most of which affect conserved protein-coding exons. The expression of many key splicing regulators changed in the course of meiosis, including downregulation of polypyrimidine tract binding protein (PTBP1) and heterogeneous nuclear RNP A1, and upregulation of nPTB, Tra2β, muscleblind, CELF proteins, Sam68 and T-STAR. The sequences near the regulated exons were significantly enriched in target sites for PTB, Tra2β and STAR proteins. Reporter minigene experiments investigating representative exons in transfected cells showed that PTB binding sites were critical for splicing of a cassette exon in the Ralgps2 mRNA and a shift in alternative 5′ splice site usage in the Bptf mRNA. We speculate that nPTB might functionally replace PTBP1 during meiosis for some target exons, with changes in the expression of other splicing factors helping to establish meiotic splicing patterns. Our data suggest that there are substantial changes in the determinants and patterns of alternative splicing in the mitotic-to-meiotic transition of the germ cell cycle.
doi:10.1093/nar/gkt811
PMCID: PMC3905889  PMID: 24038356
7.  FASCAPLYSIN as a Specific Inhibitor for CDK4: Insights from Molecular Modelling 
PLoS ONE  2012;7(8):e42612.
Cyclin-dependent kinases (CDKs) play a key role in the cell cycle and are important anti-cancer drug targets. The natural product fascaplysin inhibits CDK4 with surprising selectivity (IC50 = 0.4 µM) compared to the close homolog CDK2 (IC50 = 500 µM). Free energy calculations of the positively charged fascaplysin and an uncharged iso-electronic derivative in the CDK2 and CDK4 inhibitor complexes indicate that the positive charge of fascaplysin is crucial for selectivity. This finding will guide further improvements in the design of fascaplysin-based selective inhibitors for CDK4.
doi:10.1371/journal.pone.0042612
PMCID: PMC3419161  PMID: 22905154
8.  Acinetobacter Insertion Sequence ISAba11 Belongs to a Novel Family That Encodes Transposases with a Signature HHEK Motif 
Experimental and in silico PCR analysis targeting ISAba11 and TnAbaR islands in 196 epidemiologically unrelated Acinetobacter strains representative of ≥19 species were performed. The first two Acinetobacter baumannii ISAba11 elements identified had been found to map to the same site on TnAbaR transposons. However, no further evidence of physical linkage between the two elements was demonstrated. Indeed, examination of 25 definite or putative insertion sites suggested limited sequence specificity. Importantly, an aacC1-tagged version of ISAba11 was shown to actively transpose in A. baumannii. Similarity searches identified nine iso-ISAba11 elements in Acinetobacter and one in Enhydrobacter and single representatives of four distant homologs in bacteria belonging to the phyla “Cyanobacteria” and Proteobacteria. Phylogenetic, sequence, and structural analyses of ISAba11 and/or its associated transposase (TnpISAba11) suggested that these elements be assigned to a new family. All five homologs encode transposases with a shared extended signature comprising 16 invariant residues within the N2, N3, and C1 regions, four of which constituted the cardinal ISAba11 family HHEK motif that is substituted for the YREK DNA binding motif conserved in the IS4 family. Additionally, ISAba11 family members were associated with either no flanking direct repeat (DR) or an ISAba11-typical 5-bp DR and possessed variable-length terminal inverted repeats that exhibited extensive intrafamily sequence identity. Given the limited pairwise identity among TnpISAba11 homologs and the observed restricted distribution of ISAba11, we propose that substantial gaps persist in the evolutionary record of ISAba11 and that this element represents a recent though potentially highly significant entrant into the A. baumannii gene pool.
doi:10.1128/AEM.05663-11
PMCID: PMC3255748  PMID: 22081580
9.  Mining Genomes of Marine Cyanobacteria for Elements of Zinc Homeostasis 
Zinc is a recognized essential element for the majority of organisms, and is indispensable for the correct function of hundreds of enzymes and thousands of regulatory proteins. In aquatic photoautotrophs including cyanobacteria, zinc is thought to be required for carbonic anhydrase and alkaline phosphatase, although there is evidence that at least some carbonic anhydrases can be cambialistic, i.e., are able to acquire in vivo and function with different metal cofactors such as Co2+ and Cd2+. Given the global importance of marine phytoplankton, zinc availability in the oceans is likely to have an impact on both carbon and phosphorus cycles. Zinc concentrations in seawater vary over several orders of magnitude, and in the open oceans adopt a nutrient-like profile. Most studies on zinc handling by cyanobacteria have focused on freshwater strains and zinc toxicity; much less information is available on marine strains and zinc limitation. Several systems for zinc homeostasis have been characterized in the freshwater species Synechococcus sp. PCC 7942 and Synechocystis sp. PCC 6803, but little is known about zinc requirements or zinc handling by marine species. Comparative metallo-genomics has begun to explore not only the putative zinc proteome, but also specific protein families predicted to have an involvement in zinc homeostasis, including sensors for excess and limitation (SmtB and its homologs as well as Zur), uptake systems (ZnuABC), putative intracellular zinc chaperones (COG0523) and metallothioneins (BmtA), and efflux pumps (ZiaA and its homologs).
doi:10.3389/fmicb.2012.00142
PMCID: PMC3323870  PMID: 22514551
zinc limitation; Zur; COG0523; SmtA; BmtA
10.  Inhibition of c-Jun Kinase Provides Neuroprotection in a Model of Alzheimer’s Disease 
Neurobiology of disease  2010;39(3):311-317.
The c-Jun N-terminal kinase (JNK) pathway potentially links together the three major pathological hallmarks of Alzheimer’s disease (AD): development of amyloid plaques, neurofibrillary tangles, and brain atrophy. As activation of the JNK pathway has been observed in amyloid models of AD in association with peri-plaque regions and neuritic dystrophy, as we confirm here for Tg2576/PSM146L transgenic mice, we directly tested whether JNK inhibition could provide neuroprotection in a novel brain slice model for amyloid precursor protein (APP)-induced neurodegeneration. We found that APP/amyloid β (Aβ)-induced neurodegeneration is blocked by both small molecule and peptide inhibitors of JNK, and provide evidence that this neuroprotection occurs downstream of APP/Aβ production and processing. Our findings demonstrate that Aβ can induce neurodegeneration, at least in part, through the JNK pathway and suggest that inhibition of JNK may be of therapeutic utility in the treatment of AD.
doi:10.1016/j.nbd.2010.04.015
PMCID: PMC2910136  PMID: 20451607
JNK; APP; neurodegeneration; neuroprotection; biolistics; brain slice; drug discovery
11.  Cysteine Scanning Mutagenesis (Residues Glu52–Gly96) of the Human P2X1 Receptor for ATP 
The Journal of Biological Chemistry  2011;286(33):29207-29217.
P2X receptors are ATP-gated cation channels. The x-ray structure of a P2X4 receptor provided a major advance in understanding the molecular basis of receptor properties. However, how agonists are coordinated, the extent of the binding site, and the contribution of the vestibules in the extracellular domain to ionic permeation have not been addressed. We have used cysteine-scanning mutagenesis to determine the contribution of residues Glu52–Gly96 to human P2X1 receptor properties. ATP potency was reduced for the mutants K68C, K70C, and F92C. The efficacy of the partial agonist BzATP was also reduced for several mutants forming the back of the proposed agonist binding site. Molecular docking in silico of both ATP and BzATP provided models of the agonist binding site consistent with these data. Individual cysteine mutants had no effect or slightly increased antagonism by suramin or pyridoxal-phosphate-6-azophenyl-2′,4′-disulfonate. Mutants at the entrance to and lining the upper vestibule were unaffected by cysteine-reactive methanethiosulfonate (MTS) reagents, suggesting that it does not contribute to ionic permeation. Mutants that were sensitive to modification by MTS reagents were predominantly found either around the proposed ATP binding pocket or on the strands connecting the binding pocket to the transmembrane region and lining the central vestibule. In particular, ATP sensitivity and currents were increased by a positively charged MTS reagent at the G60C mutant at the interface between the central and extracellular vestibule. This suggests that dilation of the base of the central vestibule contributes to gating of the receptor.
doi:10.1074/jbc.M111.260364
PMCID: PMC3190727  PMID: 21690089
ATP; Ion Channels; Purinergic Agonists; Purinergic Receptor; Site-directed Mutagenesis
12.  Inhibitors of protein disulfide isomerase suppress apoptosis induced by misfolded proteins 
Nature chemical biology  2010;6(12):900-906.
A hallmark of many neurodegenerative diseases is accumulation of misfolded proteins within neurons, leading to cellular dysfunction and cell death. Although several mechanisms have been proposed to link protein misfolding to cellular toxicity, the connection remains enigmatic. Here, we report a cell death pathway involving protein disulfide isomerase (PDI), a protein chaperone that catalyzes isomerization, reduction, and oxidation of disulfides. Through a small-molecule-screening approach, we discovered five structurally distinct compounds that prevent apoptosis induced by mutant huntingtin protein. Using modified Huisgen cycloaddition chemistry, we then identified PDI as the molecular target of these small molecules. Expression of polyglutamine-expanded huntingtin exon 1 in PC12 cells caused PDI to accumulate at mitochondrial-associated-ER-membranes and trigger apoptotic cell death, via mitochondrial outer membrane permeabilization. Inhibiting PDI in rat brain cells suppressed the toxicity of mutant huntingtin exon1 and Aβ peptides processed from the amyloid precursor protein. This pro-apoptotic function of PDI provides a new mechanism linking protein misfolding and apoptotic cell death.
doi:10.1038/nchembio.467
PMCID: PMC3018711  PMID: 21079601
13.  Analogous Interactions in Initiating Complexes of the Classical and Lectin Pathways of Complement1 
The classical and lectin pathways of complement activation neutralise pathogens and stimulate key immunological processes. Both pathways are initiated by collagen-containing, soluble pattern-recognition molecules associated with specific serine proteases. In the classical pathway, C1q binds to antibody-antigen complexes or bacterial surfaces to activate C1r and C1s. In the lectin pathway, mannan-binding lectin (MBL) and ficolins bind to carbohydrates on pathogens to activate MASP-2. To characterise the interactions leading to classical pathway activation, we have analysed binding between human C1q, C1r and C1s, which associate to form C1, using full-length and truncated protease components. We show that C1r and C1s bind to C1q independently. The CUB1-EGF fragments contribute most towards binding, but CUB2 of C1r, but not of C1s, is also important. Each C1rs tetramer presents a total of six binding sites, one for each of the collagenous domains of C1q. We also demonstrate that subcomponents of the lectin and classical pathways cross-interact. Thus, although the stoichiometries of complexes differ, interactions are analogous, with equivalent contacts between recognition and protease subcomponents. Importantly, these new data are contrary to existing models of C1, and enable us to propose a new model, using MBL-MASP interactions as a template.
doi:10.4049/jimmunol.0900666
PMCID: PMC2824238  PMID: 19494295
Complement; Protein; Molecular Biology
14.  Paths reunited: initiation of the classical and lectin pathways of complement activation 
Immunobiology  2009;215(1):1-11.
Since its isolation almost fifty years ago, considerable progress has been made towards understanding the structural organisation and mode of action of C1, the initiating complex of the classical pathway of complement activation. Nevertheless, knowledge is still incomplete, especially with regard to the interactions between subcomponents, C1q, C1r and C1s, that trigger activation. Recent studies have provided new insights into these interactions, and have revealed unexpected parallels with initiating complexes of the lectin pathway of complement: MBL-MASP and ficolin-MASP. Here, we develop and expand these concepts and delineate their implications towards the key aspects of complement activation via the classical and lectin pathways.
doi:10.1016/j.imbio.2009.08.006
PMCID: PMC2824237  PMID: 19783065
15.  MicroRNA and tasiRNA diversity in mature pollen of Arabidopsis thaliana 
BMC Genomics  2009;10:643.
Background
New generation sequencing technology has allowed investigation of the small RNA populations of flowering plants at great depth. However, little is known about small RNAs in their reproductive cells, especially in post-meiotic cells of the gametophyte generation. Pollen - the male gametophyte - is the specialised haploid structure that generates and delivers the sperm cells to the female gametes at fertilisation. Whether development and differentiation of the male gametophyte depends on the action of microRNAs and trans-acting siRNAs guiding changes in gene expression is largely unknown. Here we have used 454 sequencing to survey the various small RNA populations present in mature pollen of Arabidopsis thaliana.
Results
In this study we detected the presence of 33 different microRNA families in mature pollen and validated the expression levels of 17 selected miRNAs by Q-RT-PCR. The majority of the selected miRNAs showed pollen-enriched expression compared with leaves. Furthermore, we report for the first time the presence of trans-acting siRNAs in pollen. In addition to describing new patterns of expression for known small RNAs in each of these classes, we identified 7 putative novel microRNAs. One of these, ath-MIR2939, targets a pollen-specific F-box transcript and we demonstrate cleavage of its target mRNA in mature pollen.
Conclusions
Despite the apparent simplicity of the male gametophyte, comprising just two different cell types, pollen not only utilises many miRNAs and trans-acting siRNAs expressed in the somatic tissues but also expresses novel miRNAs.
doi:10.1186/1471-2164-10-643
PMCID: PMC2808329  PMID: 20042113
16.  L1 and NCAM ADHESION MOLECULES AS SIGNALING CO-RECEPTORS IN NEURONAL MIGRATION AND PROCESS OUTGROWTH 
Current opinion in neurobiology  2008;18(3):245-250.
Summary of Recent Advances
Neural cell adhesion molecules (CAMs) of the immunoglobulin superfamily engage in multiple neuronal interactions that influence cell migration, axonal and dendritic projection, and synaptic targeting. Their downstream signal transduction events specify whether a cell moves or projects axons and dendrites to targets in the brain. Many of the diverse functions of CAMs are brought about through homophilic and heterophilic interactions with other cell surface receptors. An emerging concept is that CAMs act as co-receptors to assist in intracellular signal transduction, and to provide cytoskeletal linkage necessary for cell and growth cone motility. Here we will focus on new discoveries that have revealed novel co-receptor functions for the best understood CAMs - L1, CHL1, and NCAM- important for neuronal migration and axon guidance. We will also discuss how dysregulation of CAMs may also bear on neuropsychiatric disease and cancer.
doi:10.1016/j.conb.2008.07.015
PMCID: PMC2633433  PMID: 18760361
17.  On the Extent and Origins of Genic Novelty in the Phylum Nematoda 
Background
The phylum Nematoda is biologically diverse, including parasites of plants and animals as well as free-living taxa. Underpinning this diversity will be commensurate diversity in expressed genes, including gene sets associated specifically with evolution of parasitism.
Methods and Findings
Here we have analyzed the extensive expressed sequence tag data (available for 37 nematode species, most of which are parasites) and define over 120,000 distinct putative genes from which we have derived robust protein translations. Combined with the complete proteomes of Caenorhabditis elegans and Caenorhabditis briggsae, these proteins have been grouped into 65,000 protein families that in turn contain 40,000 distinct protein domains. We have mapped the occurrence of domains and families across the Nematoda and compared the nematode data to that available for other phyla. Gene loss is common, and in particular we identify nearly 5,000 genes that may have been lost from the lineage leading to the model nematode C. elegans. We find a preponderance of novelty, including 56,000 nematode-restricted protein families and 26,000 nematode-restricted domains. Mapping of the latest time-of-origin of these new families and domains across the nematode phylogeny revealed ongoing evolution of novelty. A number of genes from parasitic species had signatures of horizontal transfer from their host organisms, and parasitic species had a greater proportion of novel, secreted proteins than did free-living ones.
Conclusions
These classes of genes may underpin parasitic phenotypes, and thus may be targets for development of effective control measures.
Author Summary
The high-throughput sequencing of messenger RNA from parasitic organisms has permitted large-scale sequence analyses typically reserved for complete genome studies. Such expressed sequence tags (ESTs) have previously been generated for 37 species from the phylum Nematoda, of which 35 were from parasitic species. These datasets were combined with the complete genomes of Caenorhabditis elegans and C. briggsae. The sequences were assembled into 65,000 protein families, and decorated with 40,000 distinct protein domains. These annotations were analysed in the context of the nematode phylogeny. We identified massive gene loss in the model nematode, C. elegans, as well as plant-like proteins in nematodes that cause crop damage. Furthermore, many protein families were found in small groups of closely related species and may represent innovations necessary to sustain their parasitic ecologies. All of these data are presented at NemBase (www.nematodes.org) and will aid researchers working on this important group of parasites.
doi:10.1371/journal.pntd.0000258
PMCID: PMC2432500  PMID: 18596977
18.  annot8r: GO, EC and KEGG annotation of EST datasets 
BMC Bioinformatics  2008;9:180.
Background
The expressed sequence tag (EST) methodology is an attractive option for the generation of sequence data for species for which no completely sequenced genome is available. The annotation and comparative analysis of such datasets poses a formidable challenge for research groups that do not have the bioinformatics infrastructure of major genome sequencing centres. Therefore, there is a need for user-friendly tools to facilitate the annotation of non-model species EST datasets with well-defined ontologies that enable meaningful cross-species comparisons. To address this, we have developed annot8r, a platform for the rapid annotation of EST datasets with GO-terms, EC-numbers and KEGG-pathways.
Results
annot8r automatically downloads all files relevant for the annotation process and generates a reference database that stores UniProt entries, their associated Gene Ontology (GO), Enzyme Commission (EC) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) annotation and additional relevant data. For each of GO, EC and KEGG, annot8r extracts a specific sequence subset from the UniProt dataset based on the information stored in the reference database. These three subsets are then formatted for BLAST searches. The user provides the protein or nucleotide sequences to be annotated and annot8r runs BLAST searches against these three subsets. The BLAST results are parsed and the corresponding annotations retrieved from the reference database. The annotations are saved both as flat files and also in a relational postgreSQL results database to facilitate more advanced searches within the results. annot8r is integrated with the PartiGene suite of EST analysis tools.
Conclusion
annot8r is a tool that assigns GO, EC and KEGG annotations for data sets resulting from EST sequencing projects both rapidly and efficiently. The benefits of an underlying relational database, flexibility and the ease of use of the program make it ideally suited for non-model species EST-sequencing projects.
doi:10.1186/1471-2105-9-180
PMCID: PMC2324097  PMID: 18400082
19.  Developmentally regulated expression, alternative splicing and distinct sub-groupings in members of the Schistosoma mansoni venom allergen-like (SmVAL) gene family 
BMC Genomics  2008;9:89.
Background
The Sperm-coating protein/Tpx-1/Ag5/PR-1/Sc7 (SCP/TAPS) domain is found across phyla and is a major structural feature of insect allergens, mammalian sperm proteins and parasitic nematode secreted molecules. Proteins containing this domain are implicated in diverse biological activities and may be important for chronic host/parasite interactions.
Results
We report the first description of an SCP/TAPS gene family (Schistosoma mansoni venom allergen-like (SmVALs)) in the medically important Platyhelminthes (class Trematoda) and describe individual members' phylogenetic relationships, genomic organization and life cycle expression profiles. Twenty-eight SmVALs with complete SCP/TAPS domains were identified and comparison of their predicted protein features and gene structures indicated the presence of two distinct sub-families (group 1 & group 2). Phylogenetic analysis demonstrated that this group 1/group 2 split is zoologically widespread as it exists across the metazoan sub-kingdom. Chromosomal localisation and PCR analysis, coupled to inspection of the current S. mansoni genomic assembly, revealed that many of the SmVAL genes are spatially linked throughout the genome. Quantitative lifecycle expression profiling demonstrated distinct SmVAL expression patterns, including transcripts specifically associated with lifestages involved in definitive host invasion, transcripts restricted to lifestages involved in the invasion of the intermediate host and transcripts ubiquitously expressed. Analysis of SmVAL6 transcript diversity demonstrated statistically significant, developmentally regulated, alternative splicing.
Conclusion
Our results highlight the existence of two distinct SCP/TAPS protein types within the Platyhelminthes and across taxa. The extensive lifecycle expression analysis indicates several SmVAL transcripts are upregulated in infective stages of the parasite, suggesting that these particular protein products may be linked to the establishment of chronic host/parasite interactions.
doi:10.1186/1471-2164-9-89
PMCID: PMC2270263  PMID: 18294395
20.  NEMBASE: a resource for parasitic nematode ESTs 
Nucleic Acids Research  2004;32(Database issue):D427-D430.
NEMBASE (available at http://www.nematodes.org) is a publicly available online database providing access to the sequence and associated meta-data currently being generated as part of the Edinburgh–Wellcome Trust Sanger Institute parasitic nematode EST project. NEMBASE currently holds ∼100 000 sequences from 10 different species of nematode. To facilitate ease of use, sequences have been processed to generate a non-redundant set of gene objects (‘partial genome’) for each species. Users may query the database on the basis of BLAST annotation, sequence similarity or expression profiles. NEMBASE also features an interactive Java-based tool (SimiTri) which allows the simultaneous display and analysis of the relative similarity relationships of groups of sequences to three different databases. NEMBASE is currently being expanded to include sequence data from other nematode species. Other developments include access to accurate peptide predictions, improved functional annotation and incorporation of automated processes allowing rapid analysis of nematode-specific gene families.
doi:10.1093/nar/gkh018
PMCID: PMC308753  PMID: 14681449

Results 1-20 (20)