@article{kranse_beasley_adams_pires-dasilva_bell_lilley_urwin_bird_miska_smant_et al._2021, title={Toward genetic modification of plant-parasitic nematodes: delivery of macromolecules to adults and expression of exogenous mRNA in second stage juveniles}, volume={11}, ISSN={["2160-1836"]}, DOI={10.1093/g3journal/jkaa058}, abstractNote={Abstract}, number={2}, journal={G3-GENES GENOMES GENETICS}, author={Kranse, Olaf and Beasley, Helen and Adams, Sally and Pires-daSilva, Andre and Bell, Christopher and Lilley, Catherine J. and Urwin, Peter E. and Bird, David and Miska, Eric and Smant, Geert and et al.}, year={2021}, month={Feb} }
 @article{schoonmaker_hao_bird_conant_2020, title={A Single, Shared Triploidy in Three Species of Parasitic Nematodes}, volume={10}, ISSN={["2160-1836"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85077664460&partnerID=MN8TOARS}, DOI={10.1534/g3.119.400650}, abstractNote={Abstract}, number={1}, journal={G3-GENES GENOMES GENETICS}, author={Schoonmaker, Ashley and Hao, Yue and Bird, David McK. and Conant, Gavin C.}, year={2020}, month={Jan}, pages={225–233} }
 @article{yergaliyev_alexander-shani_dimerets_pivonia_bird_rachmilevitch_szitenberg_2020, title={Bacterial Community Structure Dynamics in Meloidogyne incognita-Infected Roots and Its Role in Worm-Microbiome Interactions}, volume={5}, ISSN={["2379-5042"]}, DOI={10.1128/mSphere.00306-20}, abstractNote={The study of high-resolution successional processes within tightly linked microniches is rare. Using the power and relatively low cost of metabarcoding, we describe the bacterial succession and community structure in roots infected with root-knot nematodes and in the nematodes themselves. We reveal separate successional processes in galls and adjacent non-gall root sections, which are driven by the nematode’s life cycle and the progression of the crop season. With their relatively low genetic diversity, large geographic range, spatially complex life cycle, and the simplified agricultural ecosystems they occupy, root-knot nematodes can serve as a model organism for terrestrial holobiont ecology. This perspective can improve our understanding of the temporal and spatial aspects of biological control efficacy.}, number={4}, journal={MSPHERE}, author={Yergaliyev, Timur M. and Alexander-Shani, Rivka and Dimerets, Hana and Pivonia, Shimon and Bird, David McK. and Rachmilevitch, Shimon and Szitenberg, Amir}, year={2020} }
 @article{levin_tucker_bird_mather_2020, title={Infection by cyst nematodes induces rapid remodelling of developing xylem vessels in wheat roots}, volume={10}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-020-66080-z}, abstractNote={Abstract}, number={1}, journal={SCIENTIFIC REPORTS}, author={Levin, Kara A. and Tucker, Matthew R. and Bird, David Mck. and Mather, Diane E.}, year={2020}, month={Jun} }
 @article{schreeg_marr_tarigo_sherrill_outi_scholl_bird_vigil_hung_nakajima_et al._2018, title={Identification of Cytauxzoon felis antigens via protein microarray and assessment of expression library immunization against cytauxzoonosis}, volume={15}, ISSN={["1559-0275"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85059281263&partnerID=MN8TOARS}, DOI={10.1186/s12014-018-9218-9}, abstractNote={Cytauxzoonosis is a disease of felids in North America caused by the tick-transmitted apicomplexan parasite Cytauxzoon felis. Cytauxzoonosis is particularly virulent for domestic cats, but no vaccine currently exists. The parasite cannot be cultivated in vitro, presenting a significant limitation for vaccine development.Recent sequencing of the C. felis genome has identified over 4300 putative protein-encoding genes. From this pool we constructed a protein microarray containing 673 putative C. felis proteins. This microarray was probed with sera from C. felis-infected and naïve cats to identify differentially reactive antigens which were incorporated into two expression library vaccines, one polyvalent and one monovalent. We assessed the efficacy of these vaccines to prevent of infection and/or disease in a tick-challenge model.Probing of the protein microarray resulted in identification of 30 differentially reactive C. felis antigens that were incorporated into the two expression library vaccines. However, expression library immunization failed to prevent infection or disease in cats challenged with C. felis.Protein microarray facilitated high-throughput identification of novel antigens, substantially increasing the pool of characterized C. felis antigens. These antigens should be considered for development of C. felis vaccines, diagnostics, and therapeutics.}, number={1}, journal={CLINICAL PROTEOMICS}, author={Schreeg, Megan E. and Marr, Henry S. and Tarigo, Jaime L. and Sherrill, Meredith K. and Outi, Hilton K. and Scholl, Elizabeth H. and Bird, David M. and Vigil, Adam and Hung, Chris and Nakajima, Rie and et al.}, year={2018}, month={Dec} }
 @article{holterman_karegar_mooijman_megen_elsen_vervoort_quist_karssen_decraemer_opperman_et al._2017, title={Disparate gain and loss of parasitic abilities among nematode lineages}, volume={12}, ISSN={["1932-6203"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85029856456&partnerID=MN8TOARS}, DOI={10.1371/journal.pone.0185445}, abstractNote={Plant parasitism has arisen time and again in multiple phyla, including bacteria, fungi, insects and nematodes. In most of these organismal groups, the overwhelming diversity hampers a robust reconstruction of the origins and diversification patterns of this trophic lifestyle. Being a moderately diversified phylum with ≈ 4,100 plant parasites (15% of total biodiversity) subdivided over four independent lineages, nematodes constitute a major organismal group for which the genesis of plant parasitism could be mapped. Since substantial crop losses worldwide have been attributed to less than 1% of these plant parasites, research efforts are severely biased towards this minority. With the first molecular characterisation of numerous basal and supposedly harmless plant parasites as well as their non-parasitic relatives, we were able to generate a comprehensive molecular framework that allows for the reconstruction of trophic diversification for a complete phylum. In each lineage plant parasites reside in a single taxonomic grouping (family or order), and by taking the coverage of the next lower taxonomic level as a measure for representation, 50, 67, 100 and 85% of the known diversity was included. We revealed distinct gain and loss patterns with regard to plant parasitism per se as well as host exploitation strategies between these lineages. Our map of parasitic nematode biodiversity also revealed an unanticipated time reversal in which the two most ancient lineages showed the lowest level of ecological diversification and vice versa.}, number={9}, journal={PLOS ONE}, author={Holterman, Martijn and Karegar, Akbar and Mooijman, Paul and Megen, Hanny and Elsen, Sven and Vervoort, Mariette T. W. and Quist, Casper W. and Karssen, Gerrit and Decraemer, Wilfrida and Opperman, Charles H. and et al.}, year={2017}, month={Sep} }
 @article{guo_fudali_gimeno_digennaro_chang_williamson_bird_nielsen_2017, title={Networks Underpinning Symbiosis Revealed Through Cross-Species eQTL Mapping}, volume={206}, ISSN={["1943-2631"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85027059202&partnerID=MN8TOARS}, DOI={10.1534/genetics.117.202531}, abstractNote={Abstract}, number={4}, journal={Genetics}, author={Guo, Y. and Fudali, S. and Gimeno, J. and DiGennaro, P. and Chang, S. and Williamson, V.M. and Bird, D.M. and Nielsen, D.M.}, year={2017}, pages={2175–2184} }
 @article{szitenberg_cha_opperman_bird_blaxter_lunt_2016, title={Genetic Drift, Not Life History or RNAi, Determine Long-Term Evolution of Transposable Elements}, volume={8}, ISSN={["1759-6653"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84995387797&partnerID=MN8TOARS}, DOI={10.1093/gbe/evw208}, abstractNote={Abstract Transposable elements (TEs) are a major source of genome variation across the branches of life. Although TEs may play an adaptive role in their host’s genome, they are more often deleterious, and purifying selection is an important factor controlling their genomic loads. In contrast, life history, mating system, GC content, and RNAi pathways have been suggested to account for the disparity of TE loads in different species. Previous studies of fungal, plant, and animal genomes have reported conflicting results regarding the direction in which these genomic features drive TE evolution. Many of these studies have had limited power, however, because they studied taxonomically narrow systems, comparing only a limited number of phylogenetically independent contrasts, and did not address long-term effects on TE evolution. Here, we test the long-term determinants of TE evolution by comparing 42 nematode genomes spanning over 500 million years of diversification. This analysis includes numerous transitions between life history states, and RNAi pathways, and evaluates if these forces are sufficiently persistent to affect the long-term evolution of TE loads in eukaryotic genomes. Although we demonstrate statistical power to detect selection, we find no evidence that variation in these factors influence genomic TE loads across extended periods of time. In contrast, the effects of genetic drift appear to persist and control TE variation among species. We suggest that variation in the tested factors are largely inconsequential to the large differences in TE content observed between genomes, and only by these large-scale comparisons can we distinguish long-term and persistent effects from transient or random changes.}, number={9}, journal={GENOME BIOLOGY AND EVOLUTION}, author={Szitenberg, Amir and Cha, Soyeon and Opperman, Charles H. and Bird, David M. and Blaxter, Mark L. and Lunt, David H.}, year={2016}, month={Sep}, pages={2964–2978} }
 @article{schreeg_marr_tarigo_cohn_bird_scholl_levy_wiegmann_birkenheuer_2016, title={Mitochondrial Genome Sequences and Structures Aid in the Resolution of Piroplasmida phylogeny}, volume={11}, ISSN={["1932-6203"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84994744879&partnerID=MN8TOARS}, DOI={10.1371/journal.pone.0165702}, abstractNote={The taxonomy of the order Piroplasmida, which includes a number of clinically and economically relevant organisms, is a hotly debated topic amongst parasitologists. Three genera (Babesia, Theileria, and Cytauxzoon) are recognized based on parasite life cycle characteristics, but molecular phylogenetic analyses of 18S sequences have suggested the presence of five or more distinct Piroplasmida lineages. Despite these important advancements, a few studies have been unable to define the taxonomic relationships of some organisms (e.g. C. felis and T. equi) with respect to other Piroplasmida. Additional evidence from mitochondrial genome sequences and synteny should aid in the inference of Piroplasmida phylogeny and resolution of taxonomic uncertainties. In this study, we have amplified, sequenced, and annotated seven previously uncharacterized mitochondrial genomes (Babesia canis, Babesia vogeli, Babesia rossi, Babesia sp. Coco, Babesia conradae, Babesia microti-like sp., and Cytauxzoon felis) and identified additional ribosomal fragments in ten previously characterized mitochondrial genomes. Phylogenetic analysis of concatenated mitochondrial and 18S sequences as well as cox1 amino acid sequence identified five distinct Piroplasmida groups, each of which possesses a unique mitochondrial genome structure. Specifically, our results confirm the existence of four previously identified clades (B. microti group, Babesia sensu stricto, Theileria equi, and a Babesia sensu latu group that includes B. conradae) while supporting the integration of Theileria and Cytauxzoon species into a single fifth taxon. Although known biological characteristics of Piroplasmida corroborate the proposed phylogeny, more investigation into parasite life cycles is warranted to further understand the evolution of the Piroplasmida. Our results provide an evolutionary framework for comparative biology of these important animal and human pathogens and help focus renewed efforts toward understanding the phylogenetic relationships within the group.}, number={11}, journal={PLOS ONE}, author={Schreeg, Megan E. and Marr, Henry S. and Tarigo, Jaime L. and Cohn, Leah A. and Bird, David M. and Scholl, Elizabeth H. and Levy, Michael G. and Wiegmann, Brian M. and Birkenheuer, Adam J.}, year={2016}, month={Nov} }
 @article{schreeg_marr_griffith_tarigo_bird_reichard_cohn_levy_birkenheuer_2016, title={PCR amplification of a multi-copy mitochondrial gene (cox3) improves detection of Cytauxzoon felis infection as compared to a ribosomal gene (18S)}, volume={225}, ISSN={["1873-2550"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84975504702&partnerID=MN8TOARS}, DOI={10.1016/j.vetpar.2016.06.013}, abstractNote={Cytauxzoon felis is a tick-transmitted protozoan parasite that infects felids. Clinical disease caused by acute C. felis infection rapidly progresses in domestic cats, leading to high morbidity and mortality. Accurately diagnosing cytauxzoonosis as soon as possible during acute infection would allow for earlier initiation of antiprotozoal therapy which could lead to higher survival rates. Molecular detection of parasite rRNA genes (18S) by PCR has previously been shown to be a sensitive method of diagnosing C. felis infections. Based on evidence from related apicomplexan species, we hypothesized that C. felis mitochondrial genes would exist at higher copy numbers than 18S and would be a more sensitive diagnostic target. In this study we have designed a PCR assay targeting the C. felis mitochondrial gene cytochrome c oxidase subunit III (cox3). Herein we demonstrate that (1) the cox3 PCR can detect as low as 1 copy of DNA target and can detect C. felis in samples with known mitochondrial sequence heterogeneity, (2) cox3 copy number is increased relative to 18S in blood and tissue samples from acutely infected cats, and (3) the cox3 PCR is more sensitive than 18S PCR for detection of C. felis during early infections.}, journal={VETERINARY PARASITOLOGY}, author={Schreeg, Megan E. and Marr, Henry S. and Griffith, Emily H. and Tarigo, Jaime L. and Bird, David M. and Reichard, Mason V. and Cohn, Leah A. and Levy, Michael G. and Birkenheuer, Adam J.}, year={2016}, month={Jul}, pages={123–130} }
 @book{bird_williamson_opperman_2015, title={Exploiting solved genomes of plant-parasitic nematodes to understand parasitism}, volume={73}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84925944538&partnerID=MN8TOARS}, DOI={10.1016/bs.abr.2014.12.008}, abstractNote={The growing portfolio of sequenced plant-parasitic nematodes genomes is helping to drive the research agenda for the discipline of plant nematology. Comparative genomics has confirmed much of what had been deduced from expressed sequence tag sequencing, and expanded our understanding of the extent of horizontal gene transfer as a source of novelty during the evolution of parasitism. Full catalogues have been annotated for various phytolytic and other enzymes, and the evolutionary history of those genes deduced. Beyond these direct analyses, the genome sequences serve to underpin genetic, biochemical and physiological approaches, and we suspect that this will prove to be an invaluable legacy of genome sequencing.}, journal={Advances in Botanical Research}, author={Bird, D.M. and Williamson, V.M. and Opperman, C.H.}, year={2015}, pages={241–258} }
 @article{bird_jones_opperman_kikuchi_danchin_2015, title={Signatures of adaptation to plant parasitism in nematode genomes}, volume={142}, ISSN={0031-1820 1469-8161}, url={http://dx.doi.org/10.1017/S0031182013002163}, DOI={10.1017/s0031182013002163}, abstractNote={SUMMARY}, number={S1}, journal={Parasitology}, publisher={Cambridge University Press (CUP)}, author={Bird, David Mc K. and Jones, John T. and Opperman, Charles H. and Kikuchi, Taisei and Danchin, Etienne G. J.}, year={2015}, month={Feb}, pages={S71–S84} }
 @article{burke_scholl_bird_schaff_colman_crowell_diener_gordon_graham_wang_et al._2015, title={The plant parasite Pratylenchus coffeae carries a minimal nematode genome}, volume={17}, ISSN={["1388-5545"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84938097712&partnerID=MN8TOARS}, DOI={10.1163/15685411-00002901}, abstractNote={Here we report the genome sequence of the lesion nematode, Pratylenchus coffeae, a significant pest of banana and other staple crops in tropical and sub-tropical regions worldwide. Initial analysis of the 19.67 Mb genome reveals 6712 protein encoding genes, the smallest number found in a metazoan, although sufficient to make a nematode. Significantly, no developmental or physiological pathways are obviously missing when compared to the model free-living nematode Caenorhabditis elegans, which possesses approximately 21 000 genes. The highly streamlined P. coffeae genome may reveal a remarkable functional plasticity in nematode genomes and may also indicate evolutionary routes to increased specialisation in other nematode genera. In addition, the P. coffeae genome may begin to reveal the core set of genes necessary to make a multicellular animal. Nematodes exhibit striking diversity in the niches they occupy, and the sequence of P. coffeae is a tool to begin to unravel the mechanisms that enable the extraordinary success of this phylum as both free-living and parasitic forms. Unlike the sedentary endoparasitic root-knot nematodes (Meloidogyne spp.), P. coffeae is a root-lesion nematode that does not establish a feeding site within the root. Because the P. coffeae nematode genome encodes fewer than half the number of genes found in the genomes of root-knot nematodes, comparative analysis to determine genes P. coffeae does not carry may help to define development of more sophisticated forms of nematode-plant interactions. The P. coffeae genome sequence may help to define timelines related to evolution of parasitism amongst nematodes. The genome of P. coffeae is a significant new tool to understand not only nematode evolution but animal biology in general.}, number={6}, journal={NEMATOLOGY}, author={Burke, Mark and Scholl, Elizabeth H. and Bird, David McK. and Schaff, Jennifer E. and Colman, Steven D. and Crowell, Randy and Diener, Stephen and Gordon, Oksana and Graham, Steven and Wang, Xinguo and et al.}, year={2015}, pages={621–637} }
 @article{tarigo_scholl_bird_brown_cohn_dean_levy_doolan_trieu_nordone_et al._2013, title={A Novel Candidate Vaccine for Cytauxzoonosis Inferred from Comparative Apicomplexan Genomics}, volume={8}, ISSN={["1932-6203"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84882652524&partnerID=MN8TOARS}, DOI={10.1371/journal.pone.0071233}, abstractNote={Cytauxzoonosis is an emerging infectious disease of domestic cats (Felis catus) caused by the apicomplexan protozoan parasite Cytauxzoon felis. The growing epidemic, with its high morbidity and mortality points to the need for a protective vaccine against cytauxzoonosis. Unfortunately, the causative agent has yet to be cultured continuously in vitro, rendering traditional vaccine development approaches beyond reach. Here we report the use of comparative genomics to computationally and experimentally interpret the C. felis genome to identify a novel candidate vaccine antigen for cytauxzoonosis. As a starting point we sequenced, assembled, and annotated the C. felis genome and the proteins it encodes. Whole genome alignment revealed considerable conserved synteny with other apicomplexans. In particular, alignments with the bovine parasite Theileria parva revealed that a C. felis gene, cf76, is syntenic to p67 (the leading vaccine candidate for bovine theileriosis), despite a lack of significant sequence similarity. Recombinant subdomains of cf76 were challenged with survivor-cat antiserum and found to be highly seroreactive. Comparison of eleven geographically diverse samples from the south-central and southeastern USA demonstrated 91–100% amino acid sequence identity across cf76, including a high level of conservation in an immunogenic 226 amino acid (24 kDa) carboxyl terminal domain. Using in situ hybridization, transcription of cf76 was documented in the schizogenous stage of parasite replication, the life stage that is believed to be the most important for development of a protective immune response. Collectively, these data point to identification of the first potential vaccine candidate antigen for cytauxzoonosis. Further, our bioinformatic approach emphasizes the use of comparative genomics as an accelerated path to developing vaccines against experimentally intractable pathogens.}, number={8}, journal={PLOS ONE}, author={Tarigo, Jaime L. and Scholl, Elizabeth H. and Bird, David McK and Brown, Corrie C. and Cohn, Leah A. and Dean, Gregg A. and Levy, Michael G. and Doolan, Denise L. and Trieu, Angela and Nordone, Shila K. and et al.}, year={2013}, month={Aug} }
 @article{bobay_digennaro_scholl_imin_djordjevic_mck bird_2013, title={Solution NMR studies of the plant peptide hormone CEP inform function}, volume={587}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84888642079&partnerID=MN8TOARS}, DOI={10.1016/j.febslet.2013.10.033}, abstractNote={The C‐terminally Encoded Peptide (CEP) family of regulatory peptides controls root development in vascular plants. Here, we present the first NMR structures of CEP. We show that root‐knot nematode (RKN: Meloidogyne spp.) also encodes CEP, presumably to mimic plant CEP as part of their stereotypic, parasitic interaction with vascular plants. Molecular dynamics simulations of plant‐ and nematode‐encoded CEP displaying known posttranslational modifications (PTM) provided insight into the structural effects of PTM and the conformational plasticity and rigidity of CEP. Potential mechanisms of action are discussed with respect to the structure and sampling of conformational space.}, number={24}, journal={FEBS Letters}, author={Bobay, B.G. and Digennaro, P. and Scholl, E. and Imin, N. and Djordjevic, M.A. and McK Bird, D.}, year={2013}, pages={3979–3985} }
 @article{thomas_fudali_schaff_liu_scholl_opperman_bird_williamson_2012, title={A sequence-anchored linkage map of the plant-parasitic nematode meloidogyne hapla reveals exceptionally high genome-wide recombination}, volume={2}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84883399379&partnerID=MN8TOARS}, DOI={10.1534/g3.112.002261}, abstractNote={Abstract}, number={7}, journal={G3: Genes, Genomes, Genetics}, author={Thomas, V.P. and Fudali, S.L. and Schaff, J.E. and Liu, Q. and Scholl, E.H. and Opperman, C.H. and Bird, D.M. and Williamson, V.M.}, year={2012}, pages={815–824} }
 @article{stock_bird_ghedin_goodrich-blair_2011, title={Abstracts of NEMASYM: The Third Nematode-Bacteria Symbioses Research Coordination Network Meeting}, volume={55}, ISSN={0334-5114 1878-7665}, url={http://dx.doi.org/10.1007/s13199-011-0135-1}, DOI={10.1007/s13199-011-0135-1}, number={3}, journal={Symbiosis}, publisher={Springer Science and Business Media LLC}, author={Stock, S. Patricia and Bird, David McK and Ghedin, Elodie and Goodrich-Blair, Heidi}, year={2011}, month={Nov}, pages={97–109} }
 @article{scholl_bird_2011, title={Computational and phylogenetic validation of nematode horizontal gene transfer}, volume={9}, ISSN={["1741-7007"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-79951811845&partnerID=MN8TOARS}, DOI={10.1186/1741-7007-9-9}, abstractNote={Sequencing of expressed genes has shown that nematodes, particularly the plant-parasitic nematodes, have genes purportedly acquired from other kingdoms by horizontal gene transfer. The prevailing orthodoxy is that such transfer has been a driving force in the evolution of niche specificity, and a recent paper in BMC Evolutionary Biology that presents a detailed phylogenetic analysis of cellulase genes in the free-living nematode Pristionchus pacificus at the species, genus and family levels substantiates this hypothesis.}, journal={BMC BIOLOGY}, author={Scholl, Elizabeth H. and Bird, David McK}, year={2011}, month={Feb} }
 @article{dalzell_mcveigh_warnock_mitreva_bird_abad_fleming_day_mousley_marks_et al._2011, title={RNAi Effector Diversity in Nematodes}, volume={5}, ISSN={["1935-2735"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-79959846596&partnerID=MN8TOARS}, DOI={10.1371/journal.pntd.0001176}, abstractNote={While RNA interference (RNAi) has been deployed to facilitate gene function studies in diverse helminths, parasitic nematodes appear variably susceptible. To test if this is due to inter-species differences in RNAi effector complements, we performed a primary sequence similarity survey for orthologs of 77 Caenorhabditis elegans RNAi pathway proteins in 13 nematode species for which genomic or transcriptomic datasets were available, with all outputs subjected to domain-structure verification. Our dataset spanned transcriptomes of Ancylostoma caninum and Oesophagostomum dentatum, and genomes of Trichinella spiralis, Ascaris suum, Brugia malayi, Haemonchus contortus, Meloidogyne hapla, Meloidogyne incognita and Pristionchus pacificus, as well as the Caenorhabditis species C. brenneri, C. briggsae, C. japonica and C. remanei, and revealed that: (i) Most of the C. elegans proteins responsible for uptake and spread of exogenously applied double stranded (ds)RNA are absent from parasitic species, including RNAi-competent plant-nematodes; (ii) The Argonautes (AGOs) responsible for gene expression regulation in C. elegans are broadly conserved, unlike those recruited during the induction of RNAi by exogenous dsRNA; (iii) Secondary Argonautes (SAGOs) are poorly conserved, and the nuclear AGO NRDE-3 was not identified in any parasite; (iv) All five Caenorhabditis spp. possess an expanded RNAi effector repertoire relative to the parasitic nematodes, consistent with the propensity for gene loss in nematode parasites; (v) In spite of the quantitative differences in RNAi effector complements across nematode species, all displayed qualitatively similar coverage of functional protein groups. In summary, we could not identify RNAi effector deficiencies that associate with reduced susceptibility in parasitic nematodes. Indeed, similarities in the RNAi effector complements of RNAi refractory and competent nematode parasites support the broad applicability of this research genetic tool in nematodes.}, number={6}, journal={PLOS NEGLECTED TROPICAL DISEASES}, author={Dalzell, Johnathan J. and McVeigh, Paul and Warnock, Neil D. and Mitreva, Makedonka and Bird, David McK and Abad, Pierre and Fleming, Colin C. and Day, Tim A. and Mousley, Angela and Marks, Nikki J. and et al.}, year={2011}, month={Jun} }
 @article{mbeunkui_scholl_opperman_goshe_bird_2010, title={Proteomic and Bioinformatic Analysis of the Root-Knot Nematode Meloidogyne hapla: The Basis for Plant Parasitism}, volume={9}, ISSN={1535-3893 1535-3907}, url={http://dx.doi.org/10.1021/pr1006069}, DOI={10.1021/pr1006069}, abstractNote={On the basis of the complete genome sequence of the root-knot nematode Melodogyne hapla, we have deduced and annotated the entire proteome of this plant-parasite to create a database of 14,420 proteins. We have made this database, termed HapPep3, available from the Superfamily repository of model organism proteomes (http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY). To experimentally confirm the HapPep3 assignments using proteomics, we applied a data-independent LC/MS(E) analysis to M. hapla protein extracts fractionated by SDS-PAGE. A total of 516 nonredundant proteins were identified with an average of 9 unique peptides detected per protein. Some proteins, including examples with complex gene organization, were defined by more than 20 unique peptide matches, thus, providing experimental confirmation of computational predictions of intron/exon structures. On the basis of comparisons of the broad physicochemical properties of the experimental and computational proteomes, we conclude that the identified proteins reflect a true and unbiased sampling of HapPep3. Conversely, HapPep3 appears to broadly cover the protein space able to be experimentally sampled. To estimate the false discovery rate, we queried human, plant, and bacterial databases for matches to the LC/MS(E)-derived peptides, revealing fewer than 1% of matches, most of which were to highly conserved proteins. To provide a functional comparison of the acquired and deduced proteomes, each was subjected to higher order annotation, including comparisons of Gene Ontology, protein domains, signaling, and localization predictions, further indicating concordance, although those proteins that did deviate seem to be highly significant. Approximately 20% of the experimentally sampled proteome was predicted to be secreted, and thus potentially play a role at the host-parasite interface. We examined reference pathways to determine the extent of proteome similarity of M. hapla to that of the free-living nematode, Caenorhabditis elegans, revealing significant similarities and differences. Collectively, the analyzed protein set provides an initial foundation to experimentally dissect the basis of plant parasitism by M. hapla.}, number={10}, journal={Journal of Proteome Research}, publisher={American Chemical Society (ACS)}, author={Mbeunkui, Flaubert and Scholl, Elizabeth H. and Opperman, Charles H. and Goshe, Michael B. and Bird, David McK.}, year={2010}, month={Oct}, pages={5370–5381} }
 @misc{torto-alalibo_collmer_gwinn-giglio_lindeberg_meng_chibucos_tseng_lomax_biehl_ireland_et al._2010, title={Unifying Themes in Microbial Associations with Animal and Plant Hosts Described Using the Gene Ontology}, volume={74}, ISSN={["1098-5557"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-78650086447&partnerID=MN8TOARS}, DOI={10.1128/mmbr.00017-10}, abstractNote={SUMMARYMicrobes form intimate relationships with hosts (symbioses) that range from mutualism to parasitism. Common microbial mechanisms involved in a successful host association include adhesion, entry of the microbe or its effector proteins into the host cell, mitigation of host defenses, and nutrient acquisition. Genes associated with these microbial mechanisms are known for a broad range of symbioses, revealing both divergent and convergent strategies. Effective comparisons among these symbioses, however, are hampered by inconsistent descriptive terms in the literature for functionally similar genes. Bioinformatic approaches that use homology-based tools are limited to identifying functionally similar genes based on similarities in their sequences. An effective solution to these limitations is provided by the Gene Ontology (GO), which provides a standardized language to describe gene products from all organisms. The GO comprises three ontologies that enable one to describe the molecular function(s) of gene products, the biological processes to which they contribute, and their cellular locations. Beginning in 2004, the Plant-Associated Microbe Gene Ontology (PAMGO) interest group collaborated with the GO consortium to extend the GO to accommodate terms for describing gene products associated with microbe-host interactions. Currently, over 900 terms that describe biological processes common to diverse plant- and animal-associated microbes are incorporated into the GO database. Here we review some unifying themes common to diverse host-microbe associations and illustrate how the new GO terms facilitate a standardized description of the gene products involved. We also highlight areas where new terms need to be developed, an ongoing process that should involve the whole community.}, number={4}, journal={MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS}, author={Torto-Alalibo, Trudy and Collmer, Candace W. and Gwinn-Giglio, Michelle and Lindeberg, Magdalen and Meng, Shaowu and Chibucos, Marcus C. and Tseng, Tsai-Tien and Lomax, Jane and Biehl, Bryan and Ireland, Amelia and et al.}, year={2010}, month={Dec}, pages={479–503} }
 @misc{torto-alalibo_collmer_lindeberg_bird_collmer_tyler_2009, title={Common and contrasting themes in host cell-targeted effectors from bacterial, fungal, oomycete and nematode plant symbionts described using the Gene Ontology}, volume={9}, ISSN={["1471-2180"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-60849100515&partnerID=MN8TOARS}, DOI={10.1186/1471-2180-9-s1-s3}, abstractNote={Abstract}, number={SUPPL. 1}, journal={BMC MICROBIOLOGY}, author={Torto-Alalibo, Trudy and Collmer, Candace W. and Lindeberg, Magdalen and Bird, David and Collmer, Alan and Tyler, Brett M.}, year={2009}, month={Feb} }
 @book{opperman_bird_schaff_2009, title={Genomic analysis of the root-knot nematode genome}, volume={15}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-58049157583&partnerID=MN8TOARS}, DOI={10.1007/978-3-540-85215-5_8}, abstractNote={Plant-parasitic nematodes cause substantial agricultural damage throughout the world, triggering as much as $100 billion in economic losses per year. Measures to control these pests are limited and include the use of agrichemi-cals such as methyl bromide (now available only on a “critical use exemption” basis) or the planting of crops that have natural resistance. However, the availability of chemical pesticides is decreasing and host resistance is limited. A better understanding of the complex interaction between plant-parasitic nematodes and their hosts is needed to develop new control strategies (including new chemicals). The vast majority of the damage is caused by sedentary endoparasitic forms in the order Tylenchida, which fall into clade IV of the Nematoda (Blaxter et al. 1998). In particular, the root-knot nematodes ( Meloidogyne spp.), soybean cyst nematodes ( Heterodera glycines ), and potato cyst ( Globodera spp.) nematodes are devastating parasites of plant roots.In this chapter, we will present a brief overview of the status of genomic research on root-knot nematodes. Root-knot nematodes, in particular M. hapla, are emerging as a model species for research on sedentary endoparasites. We will discuss the impact of root-knot nematodes on the host plant and focus on genomic approaches to unraveling the complex nature of the interaction from the nematode's perspective. In addition to the complete genome sequence of M. hapla, a complete genome sequence has simultaneously been obtained for the aneuploid species, M. incognita (Abad, personal communication). In the future, comparison between these two genomes will provide fundamental clues as to the evolution and biology of root-knot nematodes.}, journal={Plant Cell Monographs}, author={Opperman, C.H. and Bird, D.M. and Schaff, J.E.}, year={2009}, pages={221–237} }
 @book{bird_opperman_williamson_2009, title={Plant infection by root-knot nematode}, volume={15}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-58049175611&partnerID=MN8TOARS}, DOI={10.1007/978-3-540-85215-5_1}, abstractNote={Plant-parasitic nematodes, particularly the sedentary endoparasitic forms, are cosmopolitan pests, collectively causing over $100 billion in annual crop loss worldwide. In the past decade, significant progress has been made in identifying genes and their products that define key aspects of the host—parasite interface, including enzymes and proteins with direct roles in virulence and resistance. However, little remains known about how a host is identified or how the development of the nema-tode is coupled to establishment of the parasitic interaction. Here, we consider the role of signaling molecules and their interplay with nematode development from hatch through primary interaction with the plant.}, journal={Plant Cell Monographs}, author={Bird, D.M. and Opperman, C.H. and Williamson, V.M.}, year={2009}, pages={1–13} }
 @article{bird_williamson_abad_mccarter_danchin_castagnone-sereno_opperman_2009, title={The Genomes of Root-Knot Nematodes}, volume={47}, ISSN={["1545-2107"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-70350221931&partnerID=MN8TOARS}, DOI={10.1146/annurev-phyto-080508-081839}, abstractNote={ Plant-parasitic nematodes are the most destructive group of plant pathogens worldwide and are extremely challenging to control. The recent completion of two root-knot nematode genomes opens the way for a comparative genomics approach to elucidate the success of these parasites. Sequencing revealed that Meloidogyne hapla, a diploid that reproduces by facultative, meiotic parthenogenesis, encodes approximately 14,200 genes in a compact, 54 Mpb genome. Indeed, this is the smallest metazoan genome completed to date. By contrast, the 86 Mbp Meloidogyne incognita genome encodes approximately 19,200 genes. This species reproduces by obligate mitotic parthenogenesis and exhibits a complex pattern of aneuploidy. The genome includes triplicated regions and contains allelic pairs with exceptionally high degrees of sequence divergence, presumably reflecting adaptations to the strictly asexual reproductive mode. Both root-knot nematode genomes have compacted gene families compared with the free-living nematode Caenorhabditis elegans, and both encode large suites of enzymes that uniquely target the host plant. Acquisition of these genes, apparently via horizontal gene transfer, and their subsequent expansion and diversification point to the evolutionary history of these parasites. It also suggests new routes to their control. }, journal={ANNUAL REVIEW OF PHYTOPATHOLOGY}, author={Bird, David McK. and Williamson, Valerie M. and Abad, Pierre and McCarter, James and Danchin, Etienne G. J. and Castagnone-Sereno, Philippe and Opperman, Charles H.}, year={2009}, pages={333–351} }
 @misc{bird_opperman_2009, title={The secret(ion) life of worms}, volume={10}, ISSN={["1474-760X"]}, DOI={10.1186/gb-2009-10-1-205}, abstractNote={Tandem mass spectrographic analysis of the secreted proteins of plant- and human-parasitic nematodes reveals molecular similarities that reflect the shared need to counter host defenses.}, number={1}, journal={GENOME BIOLOGY}, author={Bird, David Mck and Opperman, Charles H.}, year={2009} }
 @article{bird_opperman_2009, title={The secret(ion) life of worms.}, volume={10}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-69449107507&partnerID=MN8TOARS}, number={1}, journal={Genome biology}, author={Bird, D.M. and Opperman, C.H.}, year={2009}, pages={205} }
 @article{schaff_mbeunkui_blackburn_bird_goshe_2008, title={A sequence-anchored genetic linkage map for the moss, Physcomitrella patens}, volume={56}, number={5}, journal={Plant Journal}, author={Schaff, J. E. and Mbeunkui, F. and Blackburn, K. and Bird, D. M. and Goshe, M. B.}, year={2008}, pages={840–854} }
 @article{schaff_mbeunkui_blackburn_bird_goshe_2008, title={SILIP: A novel stable isotope labeling method for in planta quantitative proteomic analysis}, volume={56}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-57649093858&partnerID=MN8TOARS}, DOI={10.1111/j.1365-313X.2008.03639.x}, abstractNote={Summary}, number={5}, journal={Plant Journal}, author={Schaff, J.E. and Mbeunkui, F. and Blackburn, K. and Bird, D.McK. and Goshe, M.B.}, year={2008}, pages={840–854} }
 @article{opperman_bird_williamson_rokhsar_burke_cohn_cromer_diener_gajan_graham_et al._2008, title={Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism}, volume={105}, ISSN={["1091-6490"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-54149092490&partnerID=MN8TOARS}, DOI={10.1073/pnas.0805946105}, abstractNote={
            We have established
            Meloidogyne hapla
            as a tractable model plant-parasitic nematode amenable to forward and reverse genetics, and we present a complete genome sequence. At 54 Mbp,
            M. hapla
            represents not only the smallest nematode genome yet completed, but also the smallest metazoan, and defines a platform to elucidate mechanisms of parasitism by what is the largest uncontrolled group of plant pathogens worldwide. The
            M. hapla
            genome encodes significantly fewer genes than does the free-living nematode
            Caenorhabditis elegans
            (most notably through a reduction of odorant receptors and other gene families), yet it has acquired horizontally from other kingdoms numerous genes suspected to be involved in adaptations to parasitism. In some cases, amplification and tandem duplication have occurred with genes suspected of being acquired horizontally and involved in parasitism of plants. Although
            M. hapla
            and
            C. elegans
            diverged >500 million years ago, many developmental and biochemical pathways, including those for dauer formation and RNAi, are conserved. Although overall genome organization is not conserved, there are areas of microsynteny that may suggest a primary biological function in nematodes for those genes in these areas. This sequence and map represent a wealth of biological information on both the nature of nematode parasitism of plants and its evolution.
          }, number={39}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Opperman, Charles H. and Bird, David M. and Williamson, Valerie M. and Rokhsar, Dan S. and Burke, Mark and Cohn, Jonathan and Cromer, John and Diener, Steve and Gajan, Jim and Graham, Steve and et al.}, year={2008}, month={Sep}, pages={14802–14807} }
 @article{schaff_nielsen_smith_scholl_bird_2007, title={Comprehensive Transcriptome Profiling in Tomato Reveals a Role for Glycosyltransferase in Mi-Mediated Nematode Resistance}, volume={144}, ISSN={0032-0889 1532-2548}, url={http://dx.doi.org/10.1104/pp.106.090241}, DOI={10.1104/pp.106.090241}, abstractNote={Abstract}, number={2}, journal={Plant Physiology}, publisher={American Society of Plant Biologists (ASPB)}, author={Schaff, Jennifer E. and Nielsen, Dahlia M. and Smith, Chris P. and Scholl, Elizabeth H. and Bird, David McK.}, year={2007}, month={Apr}, pages={1079–1092} }
 @article{elling_mitreva_recknor_gai_martin_maier_mcdermott_hewezi_bird_davis_et al._2007, title={Divergent evolution of arrested development in the dauer stage of Caenorhabditis elegans and the infective stage of Heterodera glycines}, volume={8}, ISSN={["1474-760X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-42949087595&partnerID=MN8TOARS}, DOI={10.1186/gb-2007-8-10-r211}, abstractNote={The soybean cyst nematode Heterodera glycines is the most important parasite in soybean production worldwide. A comprehensive analysis of large-scale gene expression changes throughout the development of plant-parasitic nematodes has been lacking to date. We report an extensive genomic analysis of H. glycines, beginning with the generation of 20,100 expressed sequence tags (ESTs). In-depth analysis of these ESTs plus approximately 1,900 previously published sequences predicted 6,860 unique H. glycines genes and allowed a classification by function using InterProScan. Expression profiling of all 6,860 genes throughout the H. glycines life cycle was undertaken using the Affymetrix Soybean Genome Array GeneChip. Our data sets and results represent a comprehensive resource for molecular studies of H. glycines. Demonstrating the power of this resource, we were able to address whether arrested development in the Caenorhabditis elegans dauer larva and the H. glycines infective second-stage juvenile (J2) exhibits shared gene expression profiles. We determined that the gene expression profiles associated with the C. elegans dauer pathway are not uniformly conserved in H. glycines and that the expression profiles of genes for metabolic enzymes of C. elegans dauer larvae and H. glycines infective J2 are dissimilar. Our results indicate that hallmark gene expression patterns and metabolism features are not shared in the developmentally arrested life stages of C. elegans and H. glycines, suggesting that developmental arrest in these two nematode species has undergone more divergent evolution than previously thought and pointing to the need for detailed genomic analyses of individual parasite species.}, number={10}, journal={GENOME BIOLOGY}, author={Elling, Axel A. and Mitreva, Makedonka and Recknor, Justin and Gai, Xiaowu and Martin, John and Maier, Thomas R. and McDermott, Jeffrey P. and Hewezi, Tarek and Bird, David Mck and Davis, Eric L. and et al.}, year={2007} }
 @article{snyder_opperman_bird_2006, title={A method for generating Meloidogyne incognita males}, volume={38}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-33750134280&partnerID=MN8TOARS}, number={2}, journal={Journal of Nematology}, author={Snyder, D.W. and Opperman, C.H. and Bird, D.Mc.K.}, year={2006}, pages={192–194} }
 @article{waterman_bird_opperman_2006, title={A method for isolation of Pasteuria penetrans endospores for bioassay and genomic studies}, volume={38}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-34248330929&partnerID=MN8TOARS}, number={1}, journal={Journal of Nematology}, author={Waterman, J.T. and Bird, D.McK. and Opperman, C.H.}, year={2006}, pages={165–167} }
 @article{bird_blaxter_mccarter_mitreva_sternberg_thomas_2006, title={A white paper on nematode comparative genomics}, volume={37}, number={4}, journal={Journal of Nematology}, author={Bird, D. M. and Blaxter, M. L. and McCarter, J. P. and Mitreva, M. and Sternberg, P. W. and Thomas, W. K.}, year={2006}, pages={408–416} }
 @article{vanholme_mitreva_van criekinge_logghe_bird_mccarter_gheysen_2006, title={Detection of putative secreted proteins in the plant-parasitic nematode Heterodera schachtii}, volume={98}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-33645243360&partnerID=MN8TOARS}, DOI={10.1007/s00436-005-0029-3}, abstractNote={The beet cyst nematode Heterodera schachtii is an important pathogen worldwide, but its molecular characterization has been limited to studying individual genes of interest. We undertook a high-throughput genomic approach and drastically increased the number of available sequences for this parasite. A total of 2,662 expressed sequence tags were grouped into 1,212 clusters representing a nonredundant catalog of H. schachtii genes. Implementing a bioinformatic workflow, we identified 50 sequences coding for candidate secreted proteins. All of these contain a putative signal peptide required for entry into the secretory pathway and lack any transmembrane domain. Included are previously postulated cell-wall-degrading enzymes and other parasitism-related genes. Moreover, we provide the first report of an arabinogalactan endo-1,4-beta-galactosidase enzyme (EC 3.2.1.89) in animals. As sequence data increase at a rapid rate, developing high-throughput genomic screening is a necessity. The in silico approach described here is an effective way to identify putative secreted proteins and prioritize candidates for further studies.}, number={5}, journal={Parasitology Research}, author={Vanholme, B. and Mitreva, M. and Van Criekinge, W. and Logghe, M. and Bird, D. and McCarter, J.P. and Gheysen, G.}, year={2006}, pages={414–424} }
 @article{mccarter_bird_mitreva_2006, title={Nematode gene sequences: Update for December 2005}, volume={37}, number={4}, journal={Journal of Nematology}, author={McCarter, J. P. and Bird, D. M. and Mitreva, M.}, year={2006}, pages={417–421} }
 @article{bird_blaxter_mccarter_mitreva_sternberg_thomas_2005, title={A white paper on nematode comparative genomics}, volume={37}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-33744994353&partnerID=MN8TOARS}, number={4}, journal={Journal of Nematology}, author={Bird, D.McK. and Blaxter, M.L. and McCarter, J.P. and Mitreva, M. and Sternberg, P.W. and Thomas, W.K.}, year={2005}, pages={408–416} }
 @misc{mitreva_blaxter_bird_mccarter_2005, title={Comparative genomics of nematodes}, volume={21}, ISSN={["1362-4555"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-24644458584&partnerID=MN8TOARS}, DOI={10.1016/j.tig.2005.08.003}, abstractNote={Recent transcriptome and genome projects have dramatically expanded the biological data available across the phylum Nematoda. Here we summarize analyses of these sequences, which have revealed multiple unexpected results. Despite a uniform body plan, nematodes are more diverse at the molecular level than was previously recognized, with many species- and group-specific novel genes. In the genus Caenorhabditis, changes in chromosome arrangement, particularly local inversions, are also rapid, with breakpoints occurring at 50-fold the rate in vertebrates. Tylenchid plant parasitic nematode genomes contain several genes closely related to genes in bacteria, implicating horizontal gene transfer events in the origins of plant parasitism. Functional genomics techniques are also moving from Caenorhabditis elegans to application throughout the phylum. Soon, eight more draft nematode genome sequences will be available. This unique resource will underpin both molecular understanding of these most abundant metazoan organisms and aid in the examination of the dynamics of genome evolution in animals.}, number={10}, journal={TRENDS IN GENETICS}, author={Mitreva, M and Blaxter, ML and Bird, DM and McCarter, JP}, year={2005}, month={Oct}, pages={573–581} }
 @article{bird_2005, title={Model systems in agriculture: Lessons from worms}, volume={146}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-16444385698&partnerID=MN8TOARS}, DOI={10.1111/j.1744-7348.2005.040066.x}, abstractNote={Summary 
 
Genomic tools are expanding the utility of organisms originally developed as models for biomedical research as a means to address complex agricultural problems. Conversely, agricultural pests are serving as models to help unravel questions of basic biology. Examples from C. elegans and root-knot nematode of this two-way exchange are discussed.}, number={2}, journal={Annals of Applied Biology}, author={Bird, D.M.}, year={2005}, pages={147–154} }
 @article{mccarter_bird_mitreva_2005, title={Nematode gene sequences: Update for December 2005}, volume={37}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-33744980477&partnerID=MN8TOARS}, number={4}, journal={Journal of Nematology}, author={McCarter, J.P. and Bird, D.McK. and Mitreva, M.}, year={2005}, pages={417–421} }
 @article{charles_carbone_davies_bird_burke_kerry_opperman_2005, title={Phylogenetic analysis of Pasteuria penetrans by use of multiple genetic loci}, volume={187}, ISSN={["1098-5530"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-23644445501&partnerID=MN8TOARS}, DOI={10.1128/JB.187.16.5700-5708.2005}, abstractNote={ABSTRACT}, number={16}, journal={JOURNAL OF BACTERIOLOGY}, author={Charles, L and Carbone, I and Davies, KG and Bird, D and Burke, M and Kerry, BR and Opperman, CH}, year={2005}, month={Aug}, pages={5700–5708} }
 @article{scholl_bird_2005, title={Resolving tylenchid evolutionary relationships through multiple gene analysis derived from EST data}, volume={36}, ISSN={["1095-9513"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-21744452353&partnerID=MN8TOARS}, DOI={10.1016/j.ympev.2005.03.016}, abstractNote={Sequence-based phylogenetic analyses typically are based on a small number of character sets and report gene trees which may not reflect the true species tree. We employed an EST mining strategy to suppress such incongruencies, and recovered the most robust phylogeny for five species of plant-parasitic nematode (Meloidogyne arenaria, M. chitwoodi, M. hapla, M. incognita, and M. javanica), three closely related tylenchid taxa (Heterodera glycines, Globodera pallida, and G. rostochiensis) and a distant taxon, Caenorhabditis elegans. Our multiple-gene approach is based on sampling more than 80,000 publicly available tylenchid EST sequences to identify phylum-wide orthologues. Bayesian inference, minimum evolution, maximum likelihood and protein distance methods were employed for phylogenetic reconstruction and hypothesis tests were constructed to elucidate differential selective pressures across the phylogeny for each gene. Our results place M. incognita and M. javanica as sister taxa, with M. arenaria as the next closely related nematode. Significant differences in selective pressure were revealed for some genes under some hypotheses, though all but one gene are exclusively under purifying selection, indicating conservation across the orthologous groups. This EST-based multi-gene analysis is a first step towards accomplishing genome-wide coverage for tylenchid evolutionary analyses.}, number={3}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Scholl, EH and Bird, DM}, year={2005}, month={Sep}, pages={536–545} }
 @article{weerasinghe_bird_allen_2005, title={Root-knot nematodes and bacterial Nod factors elicit common signal transduction events in Lotus japonicus}, volume={102}, ISSN={["0027-8424"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-14544295731&partnerID=MN8TOARS}, DOI={10.1073/pnas.0407926102}, abstractNote={
            The symbiosis responsible for nitrogen fixation in legume root nodules is initiated by rhizobial signaling molecules [Nod factors (NF)]. Using transgenically tagged microtubules and actin, we dynamically profiled the spatiotemporal changes in the cytoskeleton of living
            Lotus japonicus
            root hairs, which precede root-hair deformation and reflect one of the earliest host responses to NF. Remarkably, plant-parasitic root-knot nematodes (RKN) invoke a cytoskeletal response identical to that seen in response to NF and induce root-hair waviness and branching in legume root hairs via a signal able to function at a distance. Azide-killed nematodes do not produce this signal. A similar response to RKN was seen in tomato. Aspects of the host responses to RKN were altered or abolished by mutations in the NF receptor genes
            nfr1
            ,
            nfr5
            , and
            symRK
            , suggesting that RKN produce a molecule with functional equivalence to NF, which we name NemF. Because the ability of RKN to establish feeding sites and reproduce was markedly reduced in the mutant lines, we propose that RKN have adapted at least part of the symbiont-response pathway to enhance their parasitic ability.
          }, number={8}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Weerasinghe, RR and Bird, DM and Allen, NS}, year={2005}, month={Feb}, pages={3147–3152} }
 @article{mitreva_elling_dante_kloek_kalyanaraman_aluru_clifton_bird_baum_mccarter_2004, title={A survey of SL1-spliced transcipts from the root-lesion nematode Pratylenchus penetrans}, volume={272}, ISSN={["1617-4623"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-5644283435&partnerID=MN8TOARS}, DOI={10.1007/s00438-004-1054-0}, abstractNote={Plant-parasitic nematodes are important and cosmopolitan pathogens of crops. Here, we describe the generation and analysis of 1928 expressed sequence tags (ESTs) of a splice-leader 1 (SL1) library from mixed life stages of the root-lesion nematode Pratylenchus penetrans. The ESTs were grouped into 420 clusters and classified by function using the Gene Ontology (GO) hierarchy and the Kyoto KEGG database. Approximately 80% of all translated clusters show homology to Caenorhabditis elegans proteins, and 37% of the C. elegans gene homologs had confirmed phenotypes as assessed by RNA interference tests. Use of an SL1-PCR approach, while ensuring the cloning of the 5′ ends of mRNAs, has demonstrated bias toward short transcripts. Putative nematode-specific and Pratylenchus -specific genes were identified, and their implications for nematode control strategies are discussed.}, number={2}, journal={MOLECULAR GENETICS AND GENOMICS}, author={Mitreva, M and Elling, AA and Dante, M and Kloek, AP and Kalyanaraman, A and Aluru, S and Clifton, SW and Bird, DM and Baum, TJ and McCarter, JP}, year={2004}, month={Sep}, pages={138–148} }
 @article{lohar_schaff_laskey_kieber_bilyeu_bird_2004, title={Cytokinins play opposite roles in lateral root formation, and nematode and Rhizobial symbioses}, volume={38}, ISSN={["1365-313X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-1942507459&partnerID=MN8TOARS}, DOI={10.1111/j.1365-313X.2004.02038.x}, abstractNote={Summary}, number={2}, journal={PLANT JOURNAL}, author={Lohar, DP and Schaff, JE and Laskey, JG and Kieber, JJ and Bilyeu, KD and Bird, DM}, year={2004}, month={Apr}, pages={203–214} }
 @article{bird_2004, title={High society (of nematologists)}, volume={5}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-9444295870&partnerID=MN8TOARS}, DOI={10.1186/gb-2004-5-11-353}, abstractNote={A report on the 43rd annual meeting of the Society of Nematologists (SON), Estes Park, USA, 7-11 August 2004.}, number={11}, journal={Genome Biology}, author={Bird, D.McK.}, year={2004} }
 @misc{bird_2004, title={Signaling between nematodes and plants}, volume={7}, ISSN={["1879-0356"]}, url={https://doi.org/10.1016/j.pbi.2004.05.005}, DOI={10.1016/j.pbi.2004.05.005}, abstractNote={After hatching in the soil, root-knot nematodes must locate and penetrate a root, migrate into the vascular cylinder, and establish a permanent feeding site. Presumably, these events are accompanied by extensive signaling between the nematode parasite and the host. Hence, much emphasis has been placed on identifying proteins that are secreted by the nematode during the migratory phase. Further progress in understanding the signaling events has been made recently by studying the host response. Striking parallels can be drawn between the nematode–plant interaction and plant symbioses with other microorganisms, and evidence is emerging to suggest that nematodes acquired components of their parasitic armory from those microbes.}, number={4}, journal={CURRENT OPINION IN PLANT BIOLOGY}, author={Bird, DM}, year={2004}, month={Aug}, pages={372–376} }
 @article{mccarter_mitreva_martin_dante_wylie_rao_pape_bowers_theising_murphy_et al._2003, title={Analysis and functional classification of transcripts from the nematode Meloidogyne incognita.}, volume={4}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-9444261296&partnerID=MN8TOARS}, number={4}, journal={Genome biology}, author={McCarter, J.P. and Mitreva, M.D. and Martin, J. and Dante, M. and Wylie, T. and Rao, U. and Pape, D. and Bowers, Y. and Theising, B. and Murphy, C.V. and et al.}, year={2003}, pages={R26–1} }
 @misc{bird_kaloshian_2003, title={Are roots special? Nematodes have their say}, volume={62}, ISSN={["0885-5765"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0038374984&partnerID=MN8TOARS}, DOI={10.1016/S0885-5765(03)00045-6}, abstractNote={Nematodes are ubiquitous and cosmopolitan parasites of vascular plants, causing substantial crop damage. Although various species exploit all parts of the plant, roots are the major target. Nematodes deploy a broad spectrum of feeding strategies, ranging from simple grazing to the establishment of complex cellular structures (including galls) in host tissues. Various models of feeding site formation have been proposed, and a rôle for phytohormones has long been speculated. Based on recent molecular evidence we present several scenarios involving phytohormones in the induction of giant cells by root-knot nematodes. The origin of parasitism by nematodes, and the rôle of horizontal gene transfer from microbes is discussed. Throughout, parallels with aphid-plant interactions are emphasized.}, number={2}, journal={PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY}, author={Bird, DM and Kaloshian, I}, year={2003}, month={Feb}, pages={115–123} }
 @article{scholl_thorne_mccarter_bird_2003, title={Horizontally transferred genes in plant-parasitic nematodes: a high-throughput genomic approach.}, volume={4}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0038576862&partnerID=MN8TOARS}, number={6}, journal={Genome biology}, author={Scholl, E.H. and Thorne, J.L. and McCarter, J.P. and Bird, D.M.}, year={2003}, pages={R39–1} }
 @misc{bird_opperman_davies_2003, title={Interactions between bacteria and plant-parasitic nematodes: now and then}, volume={33}, ISSN={["1879-0135"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0042326079&partnerID=MN8TOARS}, DOI={10.1016/S0020-7519(03)00160-7}, abstractNote={Based on genome-to-genome analyses of gene sequences obtained from plant-parasitic, root-knot nematodes (Meloidogyne spp.), it seems likely that certain genes have been derived from bacteria by horizontal gene transfer. Strikingly, a common theme underpinning the function of these genes is their apparent direct relationship to the nematodes' parasitic lifestyle. Phylogenetic analyses implicate rhizobacteria as the predominant group of 'gene donor' bacteria. Root-knot nematodes and rhizobia occupy similar niches in the soil and in roots, and thus the opportunity for genetic exchange may be omnipresent. Further, both organisms establish intimate developmental interactions with host plants, and mounting evidence suggests that the mechanisms for these interactions are shared too. We propose that the origin of parasitism in Meloidogyne may have been facilitated by acquisition of genetic material from soil bacteria through horizontal transfer, and that such events represented key steps in speciation of plant-parasitic nematodes. To further understand the mechanisms of horizontal gene transfer, and also to provide experimental tools to manipulate this promising bio-control agent, we have initiated a genomic sequence of the bacterial hyper-parasite of plant parasitic nematodes, Pasteuria penetrans. Initial data have established that P. penetrans is closely related to Bacillus spp., to the extent that considerable genome synteny is apparent. Hence, Bacillus serves as a model for Pasteuria, and vice versa.}, number={11}, journal={INTERNATIONAL JOURNAL FOR PARASITOLOGY}, author={Bird, DM and Opperman, CH and Davies, KG}, year={2003}, month={Sep}, pages={1269–1276} }
 @article{lohar_bird_2003, title={Lotus japonicus: A new model to study root-parasitic nematodes}, volume={44}, ISSN={["1471-9053"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0348038676&partnerID=MN8TOARS}, DOI={10.1093/pcp/pcg146}, abstractNote={Sedentary plant-parasitic nematodes engage in complex interactions, and induce specialized feeding structures by redirecting plant developmental pathways, and parallels have been observed with rhizobial nodule development on legumes. A model legume would greatly facilitate a better understanding of the differences between parasitic (nematode) and mutualistic (rhizobia and mycorrhizae) symbioses, and we have developed Lotus japonicus as such a model. Conditions for efficient parasitism by root-knot nematode (Meloidogyne spp.) of the widely used Lotus "Gifu" ecotype were established. Features of Lotus biology, such as thin and translucent roots, proved ideal for monitoring the progress of nematode infection both on live specimens and post-staining. We examined L. japonicus mutants with nodulation phenotypes. One, har1, which is a hypernodulated mutant defective in a CLAVATA1-like receptor kinase gene, was found to be hyperinfected by M. incognita. However, another hypernodulated Lotus mutant exhibited the same level of M. incognita infection as wild-type plants. We also established conditions for infection of Lotus by soybean cyst nematode (Heterodera glycines). In contrast to the response to root-knot nematode, the Gifu ecotype is resistant to H. glycines, and elicits a hypersensitive response. This pattern of resistance recapitulates that seen on nematode-resistant soybean plants. We conclude that L. japonicus is a powerful model legume for studying compatible and incompatible plant-nematode interactions.}, number={11}, journal={PLANT AND CELL PHYSIOLOGY}, author={Lohar, DP and Bird, DM}, year={2003}, month={Nov}, pages={1176–1184} }
 @article{hirsch_bauer_bird_cullimore_tyler_yoder_2003, title={Molecular signals and receptors: Controlling rhizosphere interactions between plants and other organisms}, volume={84}, ISSN={["1939-9170"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0043094328&partnerID=MN8TOARS}, DOI={10.1890/0012-9658(2003)084[0858:msarcr]2.0.co;2}, abstractNote={Rhizosphere interactions are affected by many different regulatory signals. As yet, however, only a few have been identified. Signals, by definition, contain information, react with a receptor, and elicit a response. Signals may thus represent the highest level of evolved response in rhizosphere communities and, in that sense, occupy a supreme control point. At the same time, some signals may function as modulators of downstream responses, rather than on/off switches. To assess these possibilities, several interactions between plants and soil organisms are described, starting with the molecular interactions between legu- minous plants and symbiotic bacteria of the family Rhizobiaceae, one of the best-charac- terized plant-microbe associations in the rhizosphere. We then examine other interactions between plants and soil organisms for overlap and/or connections with the rhizosphere signals utilized in the legume-Rhizobium symbiosis. Whether information currently avail- able reflects the interaction of the organisms in nature or only in the laboratory has not always been determined. Thus, the key ecological issue of how important some of the signals are under field conditions remains to be addressed. Molecular tools now available make this task less daunting than in the past, and thus a new age of experimental field ecology may soon burst forth in rhizosphere studies. By identifying the signals, receptors, and the critical control points, we can better understand the organismal dynamics in this key belowground ecosystem.}, number={4}, journal={ECOLOGY}, author={Hirsch, AM and Bauer, WD and Bird, DM and Cullimore, J and Tyler, B and Yoder, JI}, year={2003}, month={Apr}, pages={858–868} }
 @article{mccarter_mitreva_clifton_bird_waterston_2003, title={Nematode gene sequences: Update for December 2003}, volume={35}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-1842510703&partnerID=MN8TOARS}, number={4}, journal={Journal of Nematology}, author={McCarter, J.P. and Mitreva, M. and Clifton, S.W. and Bird, D.McK. and Waterston, R.H.}, year={2003}, pages={465–469} }
 @article{mccarter_clifton_bird_waterston_2002, title={Nematode gene sequences, update for June 2002}, volume={34}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0036618995&partnerID=MN8TOARS}, number={2}, journal={Journal of Nematology}, author={McCarter, J.P. and Clifton, S.W. and Bird, D.McK. and Waterston, R.H.}, year={2002}, pages={71–74} }
 @article{koltai_bird_2002, title={Recovery and sequence validation of the histological signal following in situ RT-PCR localization of plant gene transcripts}, volume={20}, ISSN={["0735-9640"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-4544341383&partnerID=MN8TOARS}, DOI={10.1007/BF02772126}, number={4}, journal={PLANT MOLECULAR BIOLOGY REPORTER}, author={Koltai, H and Bird, DM}, year={2002}, month={Dec}, pages={391–397} }
 @article{bradshaw_bird_brown_gardiner_hirst_2001, title={Cytochrome c is not essential for viability of the fungus Aspergillus nidulans}, volume={266}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0034885798&partnerID=MN8TOARS}, DOI={10.1007/s004380100517}, abstractNote={The filamentous fungus Aspergillus nidulans is an obligate aerobe, which is capable of anaerobic survival, but not anaerobic growth. Since cytochrome c forms an essential part of the oxidative respiratory pathway it was expected that mutants lacking this component would be non-viable. Gene replacement of one homologue of the cycA (cytochrome c) gene was carried out in a diploid strain. Benomyl-induced haploidisation of this diploid yielded all cycA+ haploid colonies, initially suggesting that loss of cycA was indeed lethal. However, use of an alternative unbiased method to recover haploids yielded viable, but slow-growing, cycA- mutants. Replacement of the cycA locus in the cycA- mutants was verified by Southern blotting. Spectral analysis confirmed the absence of detectable levels of cytochrome c, and respiratory insensitivity to cyanide suggested the absence of cytochrome c-dependent respiration. Growth parameters were consistent with those expected of a CycA- mutant. Compared to the wild type, the mutants grew slowly on fermentable carbon sources, did not grow on non-fermentable carbon sources, and produced higher levels of ethanol. To our knowledge, this is the first report of a filamentous fungus that remains viable after complete elimination of a functional cytochrome c gene. We propose that the mutants are viable due to their ability to ferment and to use alternative respiratory pathways.}, number={1}, journal={Molecular Genetics and Genomics}, author={Bradshaw, R.E. and Bird, D.M. and Brown, S. and Gardiner, R.E. and Hirst, P.}, year={2001}, pages={48–55} }
 @article{koltai_dhandaydham_opperman_thomas_bird_2001, title={Overlapping plant signal transduction pathways induced by a parasitic nematode and a rhizobial endosymbiont}, volume={14}, ISSN={["0894-0282"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0034800333&partnerID=MN8TOARS}, DOI={10.1094/MPMI.2001.14.10.1168}, abstractNote={ Root-knot nematodes and rhizobia establish interactions with roots characterized by the de novo induction of host structures, termed giant cells and nodules, respectively. Two transcription regulators, PHAN and KNOX, required for the establishment of meristems were previously shown to be expressed in tomato giant cells. We isolated the orthologues of PHAN and KNOX (Mt-phan and Mt-knox-1) from the model legume Medicago truncatula, and established the spatial distribution of their expression in situ. We confirmed that Mt-phan and Mt-knox-1 are expressed in lateral root initials and in nematode-induced giant cells and showed that they are expressed in nodules induced by Sinorhizobium meliloti. Expression of both genes becomes spatially restricted as the nodules develop. We further examined nematode feeding sites for the expression of two genes involved in nodule formation, ccs52 (encodes a mitotic inhibitor) and ENOD40 (encodes an early, nodulation mitogen), and found transcripts of both genes to be present in and around giant cells induced in Medicago. Collectively, these results reveal common elements of host responses to mutualistic and parasitic plant endosymbionts and imply that overlapping regulatory pathways lead to giant cells and nodules. We discuss these pathways in the context of phytohormones and parallels between beneficial symbiosis and disease. }, number={10}, journal={MOLECULAR PLANT-MICROBE INTERACTIONS}, author={Koltai, H and Dhandaydham, M and Opperman, C and Thomas, J and Bird, D}, year={2001}, month={Oct}, pages={1168–1177} }
 @article{bird_2000, title={Alan Francis Bird: 1928-99}, volume={32}, number={1}, journal={Journal of Nematology}, author={Bird, D. M.}, year={2000}, pages={1–3} }
 @article{koltai_bird_2000, title={Epistatic repression of PHANTASTICA and class 1 KNOTTED genes is uncoupled in tomato}, volume={22}, ISSN={["0960-7412"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0034086796&partnerID=MN8TOARS}, DOI={10.1046/j.1365-313X.2000.00754.x}, abstractNote={Summary}, number={5}, journal={PLANT JOURNAL}, author={Koltai, H and Bird, DM}, year={2000}, month={Jun}, pages={455–459} }
 @article{koltai_bird_2000, title={High throughput cellular localization of specific plant mRNAs by liquid-phase in situ reverse transcription-polymerase chain reaction of tissue sections}, volume={123}, ISSN={["0032-0889"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0033836945&partnerID=MN8TOARS}, DOI={10.1104/pp.123.4.1203}, abstractNote={Abstract}, number={4}, journal={PLANT PHYSIOLOGY}, author={Koltai, H and Bird, DM}, year={2000}, month={Aug}, pages={1203–1212} }
 @article{mccarter_bird_clifton_waterston_2000, title={Nematode gene sequences, December 2000 update}, volume={32}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0034353966&partnerID=MN8TOARS}, number={4}, journal={Journal of Nematology}, author={McCarter, J.P. and Bird, D.McK. and Clifton, S.W. and Waterston, R.H.}, year={2000}, pages={331–333} }
 @article{bird_koltai_2000, title={Plant parasitic nematodes: Habitats, hormones, and horizontally-acquired genes}, volume={19}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0033758702&partnerID=MN8TOARS}, number={2}, journal={Journal of Plant Growth Regulation}, author={Bird, D.M. and Koltai, H.}, year={2000}, pages={183–194} }
 @article{mccarter_abad_jones_bird_2000, title={Rapid gene discovery in plant parasitic nematodes via Expressed Sequence Tags}, volume={2}, ISSN={["1388-5545"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0034467290&partnerID=MN8TOARS}, DOI={10.1163/156854100509574}, abstractNote={AbstractProjects currently underway are generating thousands of publicly available DNA sequences representing numerous genes from plant parasitic nematodes. Use of these data has the potential to revolutionise gene discovery, as well as aiding in genome physical mapping and expression profiling experiments. This article introduces sequences called expressed sequence tags or ESTs, which are single-sequence reads from randomly-selected cDNA clones. We review the process used to create these sequences and outline the strengths and weaknesses of ESTs as research tools. Instructions on how to access and use EST data also are provided. Découverte rapide de gènes chez les nématodes parasites des plantes: le point sur l'utilisation des Etiquettes de Séquences Exprimées - Les projets actuellement en cours génèrent des milliers de séquences d'ADN, publiquement disponibles, représentant de nombreux gènes de nématodes parasites des plantes. L'utilisation de ces données pourrait révolutionner la découverte des gènes en facilitant aussi bien les expériences de cartographie physique que celles de profils d'expression. Cet article présente les séquences dérivées de clones d'ADNc sélectionnés au hasard, appelées étiquettes de séquences exprimées (ESTs). Nous exposons le processus utilisé pour les générer de même que les avantages et les inconvénients des ESTs comme outils de recherche. Les instructions concernant l'accès et l'utilisation des ESTs sont également fournies.
         }, number={7}, journal={NEMATOLOGY}, author={McCarter, J and Abad, P and Jones, JT and Bird, D}, year={2000}, pages={719–731} }
 @misc{bird_opperman_jones_baillie_1999, title={The Caenorhabditis elegans genome: A guide in the post genomics age}, volume={37}, ISSN={["1545-2107"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0032694561&partnerID=MN8TOARS}, DOI={10.1146/annurev.phyto.37.1.247}, abstractNote={ ▪ Abstract  The completion of the entire genome sequence of the free-living nematode, Caenorhabditis elegans is a tremendous milestone in modern biology. Not only will scientists be poring over data mined from this resource, but techniques and methodologies developed along the way have changed the way we can approach biological questions. The completion of the C. elegans genomic sequence will be of particular importance to scientists working on parasitic nematodes. In many cases, these nematode species present intractable challenges to those interested in their biology and genetics. The data already compared from parasites to the C. elegans database reveals a wealth of opportunities for parasite biologists. It is likely that many of the same genes will be present in parasites and that these genes will have similar functions. Additional information regarding differences between free-living and parasitic species will provide insight into the evolution and nature of parasitism. Finally, genetic and genomic approaches to the study of parasitic nematodes now have a clearly marked path to follow. }, number={1999}, journal={ANNUAL REVIEW OF PHYTOPATHOLOGY}, author={Bird, DM and Opperman, CH and Jones, SJM and Baillie, DL}, year={1999}, pages={247–265} }
 @article{bird_opperman_1998, title={Caenorhabditis elegans: A genetic guide to parasitic nematode biology}, volume={30}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0032357095&partnerID=MN8TOARS}, number={3}, journal={Journal of Nematology}, author={Bird, D.Mck. and Opperman, C.H.}, year={1998}, pages={299–308} }
 @misc{opperman_bird_1998, title={The soybean cyst nematode, Heterodera glycines: a genetic model system for the study of plant-parasitic nematodes}, volume={1}, ISSN={["1369-5266"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0032130137&partnerID=MN8TOARS}, DOI={10.1016/1369-5266(88)80057-8}, abstractNote={Despite advances in understanding plant responses to nematode infection, little information exists regarding parasitic mechanisms. Recently, it has become possible to perform genetic analysis of soybean cyst nematode. Integration of classic and reverse genetics and genomic approaches for the parasite, with host genetics and genomics will expand our knowledge of nematode parasitism.}, number={4}, journal={CURRENT OPINION IN PLANT BIOLOGY}, author={Opperman, CH and Bird, DM}, year={1998}, month={Aug}, pages={342–346} }
 @article{bird_bradshaw_1997, title={Gene targeting is locus dependent in the filamentous fungus Aspergillus nidulans}, volume={255}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0030793387&partnerID=MN8TOARS}, DOI={10.1007/s004380050492}, abstractNote={The effect of altering the conditions of transformation on the efficiency of gene targeting in filamentous fungi was studied using Aspergillus nidulans as a model organism. The niaD and amdS genes of A. nidulans, which are both involved in nitrogen source utilisation, were selected as target loci. Homologous recombination of transforming DNA at these loci resulted in niaD and amdS mutants with an impaired ability to utilise nitrate or acetamide as the sole nitrogen source, respectively. Vectors were constructed that contained the Neurospora crassa pyr4 gene as a selectable marker and an internal segment of the amdS (0.6-1.27 kb) or niaD (0.9-2.15 kb) genes. The parameters investigated for their effect on gene targeting included (a) length of homologous DNA in the disruption cassette, (b) conformation of the transforming vector (circular or linear), (c) transcriptional status (on/off) of the targeted gene, (d) concentration of DNA in the transformation mix and (e) temperature of incubation of the transformation reaction and of protoplast regeneration on selective media. Parameters shown to have an effect on the targeting frequency at the niaD locus were tested at the amdS locus. The level of gene targeting when circular DNA was used was found to correlate with the size of the homologous segment at both loci. Similarly the level of targeting was shown to increase when vectors were linearised within the region of homology. The level of targeting was unaltered at the niaD locus when transcription was induced at different stages in the transformation procedure. Likewise, targeting was unaffected by altering the amount of DNA in the reaction mix over the concentration range tested. The regeneration temperature did have an effect on targeting, with enhanced targeting observed at 25 degrees compared with 37 degrees C. However, the most dramatic effect was the difference between targeting efficiency at different genetic loci, with targeting of niaD being at least five fold more efficient than amdS under all conditions tested.}, number={2}, journal={Molecular and General Genetics}, author={Bird, D. and Bradshaw, R.}, year={1997}, pages={219–225} }
 @article{bird_kaloshian_molinari_1997, title={Promoter structure of the RNA polymerase II large subunit gene in caenorhabditis elegans and C. Briggsae}, volume={29}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0030786968&partnerID=MN8TOARS}, number={2}, journal={Journal of Nematology}, author={Bird, D.M. and Kaloshian, I. and Molinari, S.}, year={1997}, pages={144–152} }
 @article{bird_1996, title={Manipulation of host gene expression by root-knot nematodes}, volume={82}, ISSN={["1937-2345"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0030474165&partnerID=MN8TOARS}, DOI={10.2307/3284193}, abstractNote={Root-knot nematodes (Meloidogyne spp.) establish elaborate feeding sites in their host. Unique patterns of gene expression are induced in root cells, resulting in formation of a novel cell type called a giant cell. Based on analysis of approximately 220 giant cell expressed genes, key elements of giant cell function and regulation have been identified; examples are discussed in the context of giant cell biology and ontogeny. The potential to effect nematode control by manipulating these genes in transgenic host plants is considered, and models for giant cell induction are presented.}, number={6}, journal={JOURNAL OF PARASITOLOGY}, author={Bird, DM}, year={1996}, month={Dec}, pages={881–888} }
 @article{wilson_bird_knaap_1994, title={A comprehensive subtractive cDNA cloning approach to identify nematode-induced transcripts in tomato}, volume={84}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0028096015&partnerID=MN8TOARS}, DOI={10.1094/Phyto-84-299}, abstractNote={Using a cDNA cloning technique that incorporated polymerase chain reaction amplification of cDNA and subtraction in a single-strand phage-mid vector, we constructed a library of transcripts exhibiting up regulation in tomato cells infected with the parasitic nematode Meloidogyne incognita. Starting with 51 mg of dissected, nematode-induced giant cells, we constructed a primary cDNA library of 2.2×10 6 recombinants. Subtraction against uninfected tomato roots gave a 4,860-fold enrichment. Analysis of the library as a whole indicated that contamination by nematode sequences was less than 1%. Transcripts from high copy number genes accounted for 14% of the clones; the remaining 244 recombinants appeared to be derived from distinct, unique genes [...]}, number={3}, journal={Phytopathology}, author={Wilson, M.A. and Bird, D.M. and Knaap, E.}, year={1994}, pages={299–303} }
 @article{bird_riddle_1994, title={A genetic nomenclature for parasitic nematodes}, volume={26}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0028054366&partnerID=MN8TOARS}, number={2}, journal={Journal of Nematology}, author={Bird, D.M. and Riddle, D.L.}, year={1994}, pages={138–143} }
 @article{bird_wilson_1994, title={DNA sequence and expression analysis of root-knot nematode-elicited giant cell transcripts}, volume={7}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0028428914&partnerID=MN8TOARS}, DOI={10.1094/MPMI-7-0419}, abstractNote={Fifty-eight cDNA clones isolated from a library of transcripts exhibiting up regulation in tomato root giant cells induced by infection with the parasitic nematode Meloidogyne incognita were characterized. A survey of plant tissues identified 31 transcripts present in tissues other than root, including actively dividing and expanding tissues and mature leaf tissues. The identities of approximately 20% of the giant cell transcripts were inferred from DNA sequence data; they include sequences encoding a plasmalemma proton ATPase, a putative Myb-type transcription factor, and the largest subunit of RNA polymerase II.}, number={3}, journal={Molecular Plant-Microbe Interactions}, author={Bird, D.M. and Wilson, M.A.}, year={1994}, pages={419–424} }
 @article{peloquin_bird_platzer_1993, title={Rapid miniprep isolation of mitochondrial DNA from metacestodes, and free- living and parasitic nematodes}, volume={79}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0027751334&partnerID=MN8TOARS}, DOI={10.2307/3283741}, abstractNote={A method, based on one to isolate supercoiled plasmid DNA from bacterial cells, has been developed to purify mitochondrial DNA (mtDNA) from cestode and nematode tissue easily and efficiently. Starting with as little as 100 mg of helminth tissue, sufficient mtDNA for electrophoretic analysis was extracted. This DNA was essentially free of nuclear DNA and readily digested by restriction endonucleases. Approximately 20% of the mtDNA in helminth tissue was recovered, which is a significant improvement over previously available techniques.}, number={6}, journal={Journal of Parasitology}, author={Peloquin, J.J. and Bird, D.M. and Platzer, E.G.}, year={1993}, pages={964–967} }
 @article{kaloshian_bird_1992, title={Efficient removal of hybridization signal from Southern blots probed with radiolabeled oligonucleotides}, volume={13}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0026653183&partnerID=MN8TOARS}, number={1}, journal={BioTechniques}, author={Kaloshian, I. and Bird, D.M.}, year={1992}, pages={34–36} }
 @article{bird_1992, title={Sequence comparison of the Caenorhabditis elegans dpy-13 and col-34 genes, and their deduced collagen products}, volume={120}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0026672138&partnerID=MN8TOARS}, DOI={10.1016/0378-1119(92)90102-U}, abstractNote={A 2232-nucleotide sequence spanning the col-34 gene from the nematode, Caenorhabditis elegans, is presented. This gene, which encodes a collagen protein (Clg), is transcribed from right to left with respect to the genetic map, and convergently with the nearby dpy-13 gene which also encodes a Clg. Both col-34 and dpy-13 have 5'-flanking elements in common with each other and also with other nematode Clg-encoding genes (clg). One element, variants of which are shared by col-7, col-19 and dpy-13, is predicted to be a target for a number of regulatory molecules, possibly including the ceh-18 product, a nematode POU-domain protein. The deduced amino acid sequence of Col-34 has a high degree of homology with the Dpy-13 collagen, although there are significant differences. In particular, one region of Dpy-13, which is predicted to have secondary structure different from Col-34, is altered by the recessive dpy-13(e225) mutation.}, number={2}, journal={Gene}, author={Bird, D.McK.}, year={1992}, pages={261–266} }
 @article{bird_riddle_1989, title={Molecular cloning and sequencing of ama-1, the gene encoding the largest subunit of Caenorhabditis elegans RNA polymerase II}, volume={9}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0024469811&partnerID=MN8TOARS}, DOI={10.1128/MCB.9.10.4119}, abstractNote={Two genomic sequences that share homology with Rp11215, the gene encoding the largest subunit of RNA polymerase II in Drosophila melanogaster, have been isolated from the nematode Caenorhabditis elegans. One of these sequences was physically mapped on chromosome IV within a region deleted by the deficiency mDf4, 25 kilobases (kb) from the left deficiency breakpoint. This position corresponds to ama-1 (resistance to alpha-amanitin), a gene shown previously to encode a subunit of RNA polymerase II. Northern (RNA) blotting and DNA sequencing revealed that ama-1 spans 10 kb, is punctuated by 11 introns, and encodes a 5.9-kb mRNA. A cDNA clone was isolated and partially sequenced to confirm the 3' end and several splice junctions. Analysis of the inferred 1,859-residue ama-1 product showed considerable identity with the largest subunit of RNAP II from other organisms, including the presence of a zinc finger motif near the amino terminus, and a carboxyl-terminal domain of 42 tandemly reiterated heptamers with the consensus Tyr Ser Pro Thr Ser Pro Ser. The latter domain was found to be encoded by four exons. In addition, the sequence oriented ama-1 transcription with respect to the genetic map. The second C. elegans sequence detected with the Drosophila probe, named rpc-1, was found to encode a 4.8-kb transcript and hybridized strongly to the gene encoding the largest subunit of RNA polymerase III from yeast, implicating rpc-1 as encoding the analogous peptide in the nematode. By contrast with ama-1, rpc-1 was not deleted by mDf4 or larger deficiencies examined, indicating that these genes are no closer than 150 kb. Genes flanking ama-1, including two collagen genes, also have been identified.}, number={10}, journal={Molecular and Cellular Biology}, author={Bird, D.M. and Riddle, D.L.}, year={1989}, pages={4119–4130} }
 @article{mende_bird_albert_riddle_1988, title={dpy-13: A nematode collagen gene that affects body shape}, volume={55}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0024291340&partnerID=MN8TOARS}, DOI={10.1016/0092-8674(88)90215-2}, abstractNote={Mutations in the Caenorhabditis elegans dpy-13 (dumpy) gene result in a short, chunky body shape. This gene was tagged by insertion of the Tc1 transposon, and the wild-type gene was cloned by chromosomal walking 11 kb from ama-1, a cloned gene encoding the large subunit of RNA polymerase II. Three transposon insertion sites in dpy-13 are located near the 5' end of a 1.2 kb transcribed region. The EMS-induced reference allele, dpy-13(e184), carries a small deletion near the middle of this gene. The DNA sequence reveals that dpy-13 is a member of the collagen multi-gene family, and it could encode a polypeptide of 302 amino acids. A 146 base pair sequence, encoding amino acids 56-103, is unique in the C. elegans genome, and it hybridizes to a 1 kb mRNA of moderate abundance.}, number={4}, journal={Cell}, author={Mende, N. and Bird, D.Mck. and Albert, P.S. and Riddle, D.L.}, year={1988}, pages={567–576} }