@article{schiffman_scholl_furey_nagle_2023, title={Toxicological and pharmacokinetic properties of sucralose-6-acetate and its parent sucralose: <i>in vitro</i> screening assays}, volume={5}, ISSN={1093-7404 1521-6950}, url={http://dx.doi.org/10.1080/10937404.2023.2213903}, DOI={10.1080/10937404.2023.2213903}, abstractNote={The purpose of this study was to determine the toxicological and pharmacokinetic properties of sucralose-6-acetate, a structural analog of the artificial sweetener sucralose. Sucralose-6-acetate is an intermediate and impurity in the manufacture of sucralose, and recent commercial sucralose samples were found to contain up to 0.67% sucralose-6-acetate. Studies in a rodent model found that sucralose-6-acetate is also present in fecal samples with levels up to 10% relative to sucralose which suggest that sucralose is also acetylated in the intestines. A MultiFlow® assay, a high-throughput genotoxicity screening tool, and a micronucleus (MN) test that detects cytogenetic damage both indicated that sucralose-6-acetate is genotoxic. The mechanism of action was classified as clastogenic (produces DNA strand breaks) using the MultiFlow® assay. The amount of sucralose-6-acetate in a single daily sucralose-sweetened drink might far exceed the threshold of toxicological concern for genotoxicity (TTCgenotox) of 0.15 µg/person/day. The RepliGut® System was employed to expose human intestinal epithelium to sucralose-6-acetate and sucralose, and an RNA-seq analysis was performed to determine gene expression induced by these exposures. Sucralose-6-acetate significantly increased the expression of genes associated with inflammation, oxidative stress, and cancer with greatest expression for the metallothionein 1 G gene (MT1G). Measurements of transepithelial electrical resistance (TEER) and permeability in human transverse colon epithelium indicated that sucralose-6-acetate and sucralose both impaired intestinal barrier integrity. Sucralose-6-acetate also inhibited two members of the cytochrome P450 family (CYP1A2 and CYP2C19). Overall, the toxicological and pharmacokinetic findings for sucralose-6-acetate raise significant health concerns regarding the safety and regulatory status of sucralose itself.}, journal={Journal of Toxicology and Environmental Health, Part B}, publisher={Informa UK Limited}, author={Schiffman, Susan S. and Scholl, Elizabeth H. and Furey, Terrence S. and Nagle, H. Troy}, year={2023}, month={May}, pages={1–35} }
 @article{zhou_gallins_etheridge_jima_scholl_wright_innocenti_2022, title={A resource for integrated genomic analysis of the human liver}, volume={12}, ISSN={["2045-2322"]}, url={https://doi.org/10.1038/s41598-022-18506-z}, DOI={10.1038/s41598-022-18506-z}, abstractNote={In this study, we generated whole-transcriptome RNA-Seq from n = 192 genotyped liver samples and used these data with existing data from the GTEx Project (RNA-Seq) and previous liver eQTL (microarray) studies to create an enhanced transcriptomic sequence resource in the human liver. Analyses of genotype-expression associations show pronounced enrichment of associations with genes of drug response. The associations are primarily consistent across the two RNA-Seq datasets, with some modest variation, indicating the importance of obtaining multiple datasets to produce a robust resource. We further used an empirical Bayesian model to compare eQTL patterns in liver and an additional 20 GTEx tissues, finding that MHC genes, and especially class II genes, are enriched for liver-specific eQTL patterns. To illustrate the utility of the resource to augment GWAS analysis with small sample sizes, we developed a novel meta-analysis technique to combine several liver eQTL data sources. We also illustrate its application using a transcriptome-enhanced re-analysis of a study of neutropenia in pancreatic cancer patients. The associations of genotype with liver expression, including splice variation and its genetic associations, are made available in a searchable genome browser.}, number={1}, journal={SCIENTIFIC REPORTS}, author={Zhou, Yi-Hui and Gallins, Paul J. and Etheridge, Amy S. and Jima, Dereje and Scholl, Elizabeth and Wright, Fred A. and Innocenti, Federico}, year={2022}, month={Sep} }
 @article{zakas_harry_scholl_rockman_2022, title={The Genome of the Poecilogonous Annelid Streblospio benedicti}, volume={14}, ISSN={["1759-6653"]}, url={https://doi.org/10.1093/gbe/evac008}, DOI={10.1093/gbe/evac008}, abstractNote={Streblospio benedicti is a common marine annelid that has become an important model for developmental evolution. It is the only known example of poecilogony (where two distinct developmental modes occur within a single species) that is due to a heritable difference in egg size. The dimorphic developmental programs and life-histories exhibited in this species depend on differences within the genome, making it an optimal model for understanding the genomic basis of developmental divergence. Studies using S. benedicti have begun to uncover the genetic and genomic principles that underlie developmental uncoupling, but until now they have been limited by the lack of availability of genomic tools. Here, we present an annotated chromosomal-level genome assembly of S. benedicti generated from a combination of Illumina reads, Nanopore long reads, Chicago and Hi-C chromatin interaction sequencing, and a genetic map from experimental crosses. At 701.4 Mb, the S. benedicti genome is the largest annelid genome to date that has been assembled to chromosomal scaffolds. The complete genome of S. benedicti is valuable for functional genomic analyses of development and evolution, as well as phylogenetic comparison within the annelida and the Lophotrochozoa. Despite having two developmental modes, there is no evidence of genome duplication or substantial gene number expansions. Instead, lineage-specific repeats account for much of the expansion of this genome compared with other annelids.}, number={2}, journal={GENOME BIOLOGY AND EVOLUTION}, author={Zakas, Christina and Harry, Nathan D. and Scholl, Elizabeth H. and Rockman, Matthew V}, editor={Lavrov, DennisEditor}, year={2022}, month={Feb} }
 @article{davis_belikoff_dickey_scholl_benoit_scott_2021, title={Genome and transcriptome sequencing of the green bottle fly, Lucilia sericata, reveals underlying factors of sheep flystrike and maggot debridement therapy}, volume={113}, ISSN={["1089-8646"]}, DOI={10.1016/j.ygeno.2021.10.003}, abstractNote={The common green bottle blow fly Lucilia sericata (family, Calliphoridae) is widely used for maggot debridement therapy, which involves the application of sterile maggots to wounds. The larval excretions and secretions are important for consuming necrotic tissue and inhibiting bacterial growth in wounds of patients. Lucilia sericata is also of importance as a pest of sheep and in forensic studies to estimate a postmortem interval. Here we report the assembly of a 565.3 Mb genome from long read PacBio DNA sequencing of genomic DNA. The genome contains 14,704 predicted protein coding genes and 1709 non-coding genes. Targeted annotation and transcriptional analyses identified genes that are highly expressed in the larval salivary glands (secretions) and Malpighian tubules (excretions) under normal growth conditions and following heat stress. The genomic resources will underpin future genetic studies and in development of engineered strains for genetic control of L. sericata and for biotechnology-enhanced maggot therapy.}, number={6}, journal={GENOMICS}, author={Davis, Rebecca J. and Belikoff, Esther J. and Dickey, Allison N. and Scholl, Elizabeth H. and Benoit, Joshua B. and Scott, Maxwell J.}, year={2021}, month={Nov}, pages={3978–3988} }
 @article{holmes_scholl_dickey_hess_2021, title={High-resolution characterization of the structural features and genetic variation of six feline leukocyte antigen class I loci via single molecule, real-time (SMRT) sequencing}, volume={6}, ISSN={["1432-1211"]}, DOI={10.1007/s00251-021-01221-w}, journal={IMMUNOGENETICS}, author={Holmes, Jennifer C. and Scholl, Elizabeth H. and Dickey, Allison N. and Hess, Paul R.}, year={2021}, month={Jun} }
 @article{meinders_mendoza_dickey_scholl_hassan_2020, title={Complete Genome Sequences of Six Lactobacilli Isolated from American Quarter Horses}, volume={9}, ISSN={["2576-098X"]}, url={https://doi.org/10.1128/MRA.00997-20}, DOI={10.1128/MRA.00997-20}, abstractNote={We report the complete circular genome sequences of six Lactobacillus strains and their plasmids, if any, from the fecal material of quarter horses at different ages.}, number={47}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, publisher={American Society for Microbiology}, author={Meinders, Rachael I. and Mendoza, Mary and Dickey, Allison N. and Scholl, Elizabeth H. and Hassan, Hosni M.}, editor={Rasko, DavidEditor}, year={2020}, month={Nov} }
 @article{scott_benoit_davis_bailey_varga_martinson_hickner_syed_cardoso_torres_et al._2020, title={Genomic analyses of a livestock pest, the New World screwworm, find potential targets for genetic control programs}, volume={3}, ISSN={["2399-3642"]}, DOI={10.1038/s42003-020-01152-4}, abstractNote={Abstract The New World Screwworm fly, Cochliomyia hominivorax , is a major pest of livestock in South America and Caribbean. However, few genomic resources have been available for this species. A genome of 534 Mb was assembled from long read PacBio DNA sequencing of DNA from a highly inbred strain. Analysis of molecular evolution identified 40 genes that are likely under positive selection. Developmental RNA-seq analysis identified specific genes associated with each stage. We identify and analyze the expression of genes that are likely important for host-seeking behavior (chemosensory), development of larvae in open wounds in warm-blooded animals (heat shock protein, immune response) and for building transgenic strains for genetic control programs including gene drive (sex determination, germline). This study will underpin future experiments aimed at understanding the parasitic lifestyle of the screwworm fly and greatly facilitate future development of strains for efficient systems for genetic control of screwworm.}, number={1}, journal={COMMUNICATIONS BIOLOGY}, author={Scott, Maxwell J. and Benoit, Joshua B. and Davis, Rebecca J. and Bailey, Samuel T. and Varga, Virag and Martinson, Ellen O. and Hickner, Paul V and Syed, Zainulabeuddin and Cardoso, Gisele A. and Torres, Tatiana T. and et al.}, year={2020}, month={Aug} }
 @article{singleton_lee_dickey_stroud_scholl_wright_aitken_2018, title={Polyphasic characterization of four soil-derived phenanthrene-degrading Acidovorax strains and proposal of Acidovorax carolinensis sp nov.}, volume={41}, ISSN={["0723-2020"]}, DOI={10.1016/j.syapm.2018.06.001}, abstractNote={Four bacterial strains identified as members of the Acidovorax genus were isolated from two geographically distinct but similarly contaminated soils in North Carolina, USA, characterized, and their genomes sequenced. Their 16S rRNA genes were highly similar to those previously recovered during stable-isotope probing (SIP) of one of the soils with the polycyclic aromatic hydrocarbon (PAH) phenanthrene. Heterotrophic growth of all strains occurred with a number of organic acids, as well as phenanthrene, but no other tested PAHs. Optimal growth occurred aerobically under mesophilic temperature, neutral pH, and low salinity conditions. Predominant fatty acids were C16:1ω7c/C16:1ω6c, C16:0, and C18:1ω7c, and were consistent with the genus. Genomic G+C contents ranged from 63.6 to 64.2%. A combination of whole genome comparisons and physiological analyses indicated that these four strains likely represent a single species within the Acidovorax genus. Chromosomal genes for phenanthrene degradation to phthalate were nearly identical to highly conserved regions in phenanthrene-degrading Delftia, Burkholderia, Alcaligenes, and Massilia species in regions flanked by transposable or extrachromosomal elements. The lower degradation pathway for phenanthrene metabolism was inferred by comparisons to described genes and proteins. The novel species Acidovorax carolinensis sp. nov. is proposed, comprising the four strains described in this study with strain NA3T as the type strain (=LMG 30136, =DSM 105008).}, number={5}, journal={SYSTEMATIC AND APPLIED MICROBIOLOGY}, author={Singleton, David R. and Lee, Janice and Dickey, Allison N. and Stroud, Aaron and Scholl, Elizabeth H. and Wright, Fred A. and Aitken, Michael D.}, year={2018}, month={Sep}, pages={460–472} }
 @article{balik-meisner_truong_scholl_tanguay_reif_2018, title={Population genetic diversity in zebrafish lines}, volume={29}, ISSN={["1432-1777"]}, url={https://doi.org/10.1007/s00335-018-9735-x}, DOI={10.1007/s00335-018-9735-x}, abstractNote={Toxicological and pharmacological researchers have seized upon the many benefits of zebrafish, including the short generation time, well-characterized development, and early maturation as clear embryos. A major difference from many model organisms is that standard husbandry practices in zebrafish are designed to maintain population diversity. While this diversity is attractive for translational applications in human and ecological health, it raises critical questions on how interindividual genetic variation might contribute to chemical exposure or disease susceptibility differences. Findings from pooled samples of zebrafish support this supposition of diversity yet cannot directly measure allele frequencies for reference versus alternate alleles. Using the Tanguay lab Tropical 5D zebrafish line (T5D), we performed whole genome sequencing on a large group (n = 276) of individual zebrafish embryos. Paired-end reads were collected on an Illumina 3000HT, then aligned to the most recent zebrafish reference genome (GRCz10). These data were used to compare observed population genetic variation across species (humans, mice, zebrafish), then across lines within zebrafish. We found more single nucleotide polymorphisms (SNPs) in T5D than have been reported in SNP databases for any of the WIK, TU, TL, or AB lines. We theorize that some subset of the novel SNPs may be shared with other zebrafish lines but have not been identified in other studies due to the limitations of capturing population diversity in pooled sequencing strategies. We establish T5D as a model that is representative of diversity levels within laboratory zebrafish lines and demonstrate that experimental design and analysis can exert major effects when characterizing genetic diversity in heterogeneous populations.}, number={1-2}, journal={MAMMALIAN GENOME}, publisher={Springer Science and Business Media LLC}, author={Balik-Meisner, Michele and Truong, Lisa and Scholl, Elizabeth H. and Tanguay, Robert L. and Reif, David M.}, year={2018}, month={Feb}, pages={90–100} }
 @article{davis_belikoff_scholl_li_scott_2018, title={no blokes Is Essential for Male Viability and X Chromosome Gene Expression in the Australian Sheep Blowfly}, volume={28}, ISSN={["1879-0445"]}, DOI={10.1016/j.cub.2018.05.005}, abstractNote={It has been hypothesized that the Drosophila 4th chromosome is derived from an ancient X chromosome [1Vicoso B. Bachtrog D. Reversal of an ancient sex chromosome to an autosome in Drosophila.Nature. 2013; 499: 332-335Crossref PubMed Scopus (131) Google Scholar]. In the Australian sheep blowfly, Lucilia cuprina, the heterochromatic X chromosome contains few active genes and orthologs of Drosophila X-linked genes are autosomal. Of 8 X-linked genes identified previously in L. cuprina, 6 were orthologs of Drosophila 4th-chromosome genes [2Linger R.J. Belikoff E.J. Scott M.J. Dosage compensation of X-linked Muller element F genes but not X-linked transgenes in the Australian sheep blowfly.PLoS ONE. 2015; 10: e0141544Crossref PubMed Scopus (14) Google Scholar]. The X-linked genes were expressed equally in males and females. Here we identify an additional 51 X-linked genes and show that most are dosage compensated. Orthologs of 49 of the 59 X-linked genes are on the 4th chromosome in D. melanogaster. Because painting of fourth (Pof) is important for expression of Drosophila 4th-chromosome genes [3Johansson A.M. Stenberg P. Allgardsson A. Larsson J. POF regulates the expression of genes on the fourth chromosome in Drosophila melanogaster by binding to nascent RNA.Mol. Cell. Biol. 2012; 32: 2121-2134Crossref PubMed Scopus (27) Google Scholar], we used Cas9 to make a loss-of-function knockin mutation in an L. cuprina Pof ortholog we call no blokes (nbl). Homozygous nbl males derived from homozygous nbl mothers die at the late pupal stage. Homozygous nbl females are viable, fertile, and live longer than heterozygous nbl females. RNA expression of most X-linked genes was reduced in homozygous nbl male pupae and to a lesser extent in nbl females compared to heterozygous siblings. The results suggest that NBL could be important for X chromosome dosage compensation in L. cuprina. NBL may also facilitate gene expression in the heterochromatic environment of the X chromosome in both sexes. This study supports the hypothesis on the origin of the Drosophila 4th chromosome and that a POF-like protein was required for normal gene expression on the ancient X chromosome.}, number={12}, journal={CURRENT BIOLOGY}, author={Davis, Rebecca J. and Belikoff, Esther J. and Scholl, Elizabeth H. and Li, Fang and Scott, Maxwell J.}, year={2018}, month={Jun}, pages={1987-+} }
 @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{borst_suyemoto_scholl_fuller_barnes_2015, title={Comparative Genomic Analysis Identifies Divergent Genomic Features of Pathogenic Enterococcus cecorum Including a Type IC CRISPR-Cas System, a Capsule Locus, an epa-Like Locus, and Putative Host Tissue Binding Proteins}, volume={10}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0121294}, abstractNote={Enterococcus cecorum (EC) is the dominant enteric commensal of adult chickens and contributes to the gut consortia of many avian and mammalian species. While EC infection is an uncommon zoonosis, like other enterococcal species it can cause life-threating nosocomial infection in people. In contrast to other enterococci which are considered opportunistic pathogens, emerging pathogenic strains of EC cause outbreaks of musculoskeletal disease in broiler chickens. Typical morbidity and mortality is comparable to other important infectious diseases of poultry. In molecular epidemiologic studies, pathogenic EC strains were found to be genetically clonal. These findings suggested acquisition of specific virulence determinants by pathogenic EC. To identify divergent genomic features and acquired virulence determinants in pathogenic EC; comparative genomic analysis was performed on genomes of 3 pathogenic and 3 commensal strains of EC. Pathogenic isolates had smaller genomes with a higher GC content, and they demonstrated large regions of synteny compared to commensal isolates. A molecular phylogenetic analysis demonstrated sequence divergence in pathogenic EC genomes. At a threshold of 98% identity, 414 predicted proteins were identified that were highly conserved in pathogenic EC but not in commensal EC. Among these, divergent CRISPR-cas defense loci were observed. In commensal EC, the type IIA arrangement typical for enterococci was present; however, pathogenic EC had a type IC locus, which is novel in enterococci but commonly observed in streptococci. Potential mediators of virulence identified in this analysis included a polysaccharide capsular locus similar to that recently described for E. faecium, an epa-like locus, and cell wall associated proteins which may bind host extracellular matrix. This analysis identified specific genomic regions, coding sequences, and predicted proteins which may be related to the divergent evolution and increased virulence of emerging pathogenic strains of EC.}, number={4}, journal={PLOS ONE}, author={Borst, Luke B. and Suyemoto, M. Mitsu and Scholl, Elizabeth H. and Fuller, Fredrick J. and Barnes, H. John}, year={2015}, month={Apr} }
 @article{hecht_scholl_walker_taylor_cliby_motsinger-reif_muddiman_2015, title={Relative Quantification and Higher-Order Modeling of the Plasma Glycan Cancer Burden Ratio in Ovarian Cancer Case-Control Samples}, volume={14}, ISSN={["1535-3907"]}, DOI={10.1021/acs.jproteome.5b00703}, abstractNote={An early-stage, population-wide biomarker for ovarian cancer (OVC) is essential to reverse its high mortality rate. Aberrant glycosylation by OVC has been reported, but studies have yet to identify an N-glycan with sufficiently high specificity. We curated a human biorepository of 82 case-control plasma samples, with 27%, 12%, 46%, and 15% falling across stages I–IV, respectively. For relative quantitation, glycans were analyzed by the individuality normalization when labeling with glycan hydrazide tags (INLIGHT) strategy for enhanced electrospray ionization, MS/MS analysis. Sixty-three glycan cancer burden ratios (GBRs), defined as the log10 ratio of the case-control extracted ion chromatogram abundances, were calculated above the limit of detection. The final GBR models, built using stepwise forward regression, included three significant terms: OVC stage, normalized mean GBR, and tag chemical purity; glycan class, fucosylation, or sialylation were not significant variables. After Bonferroni correction, seven N-glycans were identified as significant (p < 0.05), and after false discovery rate correction, an additional four glycans were determined to be significant (p < 0.05), with one borderline (p = 0.05). For all N-glycans, the vectors of the effects from stages II–IV were sequentially reversed, suggesting potential biological changes in OVC morphology or in host response.}, number={10}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Hecht, Elizabeth S. and Scholl, Elizabeth H. and Walker, S. Hunter and Taylor, Amber D. and Cliby, William A. and Motsinger-Reif, Alison A. and Muddiman, David C.}, year={2015}, month={Oct}, pages={4394–4401} }
 @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{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.See research article: http://www.biomedcentral.com/1471-2148/11/13}, journal={BMC BIOLOGY}, author={Scholl, Elizabeth H. and Bird, David McK}, year={2011}, month={Feb} }
 @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={Root-knot nematode (RKN; Meloidogyne spp.) is a major crop pathogen worldwide. Effective resistance exists for a few plant species, including that conditioned by Mi in tomato (Solanum lycopersicum). We interrogated the root transcriptome of the resistant (Mi+) and susceptible (Mi-) cultivars 'Motelle' and 'Moneymaker,' respectively, during a time-course infection by the Mi-susceptible RKN species Meloidogyne incognita and the Mi-resistant species Meloidogyne hapla. In the absence of RKN infection, only a single significantly regulated gene, encoding a glycosyltransferase, was detected. However, RKN infection influenced the expression of broad suites of genes; more than half of the probes on the array identified differential gene regulation between infected and uninfected root tissue at some stage of RKN infection. We discovered 217 genes regulated during the time of RKN infection corresponding to establishment of feeding sites, and 58 genes that exhibited differential regulation in resistant roots compared to uninfected roots, including the glycosyltransferase. Using virus-induced gene silencing to silence the expression of this gene restored susceptibility to M. incognita in 'Motelle,' indicating that this gene is necessary for resistance to RKN. Collectively, our data provide a picture of global gene expression changes in roots during compatible and incompatible associations with RKN, and point to candidates for further investigation.}, 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{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} }