@article{hassan_mendoza_dickey_2024, title={Complete genome sequences of <i>Lactobacillus acidophilus</i> strain P42 and <i>Limosilactobacillus reuteri</i> strain P43 isolated from chicken cecum}, volume={3}, ISSN={["2576-098X"]}, url={https://doi.org/10.1128/mra.01140-23}, DOI={10.1128/mra.01140-23}, abstractNote={ABSTRACT}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Hassan, Hosni M. and Mendoza, Mary and Dickey, Allison N.}, editor={Hotopp, Julie C. DunningEditor}, year={2024}, month={Mar} }
 @article{sakolish_moyer_tsai_ford_dickey_wright_han_bajaj_baltazar_carmichael_et al._2023, title={Analysis of reproducibility and robustness of a renal proximal tubule microphysiological system OrganoPlate 3-lane 40 for in vitro studies of drug transport and toxicity}, ISSN={["1096-0929"]}, DOI={10.1093/toxsci/kfad080}, abstractNote={Abstract}, journal={TOXICOLOGICAL SCIENCES}, author={Sakolish, Courtney and Moyer, Haley L. and Tsai, Han-Hsuan D. and Ford, Lucie C. and Dickey, Allison N. and Wright, Fred A. and Han, Gang and Bajaj, Piyush and Baltazar, Maria T. and Carmichael, Paul L. and et al.}, year={2023}, month={Aug} }
 @article{dewey_selote_griffin_dickey_jantz_smith_matthiadis_strable_kestell_smith_2023, title={Cytoplasmic male sterility and abortive seed traits generated through mitochondrial genome editing coupled with allotopic expression of atp1 in tobacco}, volume={14}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2023.1253640}, abstractNote={Allotopic expression is the term given for the deliberate relocation of gene function from an organellar genome to the nuclear genome. We hypothesized that the allotopic expression of an essential mitochondrial gene using a promoter that expressed efficiently in all cell types except those responsible for male reproduction would yield a cytoplasmic male sterility (CMS) phenotype once the endogenous mitochondrial gene was inactivated via genome editing. To test this, we repurposed the mitochondrially encoded atp1 gene of tobacco to function in the nucleus under the transcriptional control of a CaMV 35S promoter (construct 35S:nATP1), a promoter that has been shown to be minimally expressed in early stages of anther development. The endogenous atp1 gene was eliminated (Δatp1) from 35S:nATP1 tobacco plants using custom-designed meganucleases directed to the mitochondria. Vegetative growth of most 35S:nATP1/Δatp1 plants appeared normal, but upon flowering produced malformed anthers that failed to shed pollen. When 35S:nATP1/Δatp1 plants were cross-pollinated, ovary/capsule development appeared normal, but the vast majority of the resultant seeds were small, largely hollow and failed to germinate, a phenotype akin to the seedless trait known as stenospermocarpy. Characterization of the mitochondrial genomes from three independent Δatp1 events suggested that spontaneous recombination over regions of microhomology and substoichiometric shifting were the mechanisms responsible for atp1 elimination and genome rearrangement in response to exposure to the atp1-targeting meganucleases. Should the results reported here in tobacco prove to be translatable to other crop species, then multiple applications of allotopic expression of an essential mitochondrial gene followed by its elimination through genome editing can be envisaged. Depending on the promoter(s) used to drive the allotopic gene, this technology may have potential application in the areas of: (1) CMS trait development for use in hybrid seed production; (2) seedless fruit production; and (3) transgene containment.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Dewey, Ralph E. and Selote, Devarshi and Griffin, H. Carol and Dickey, Allison N. and Jantz, Derek and Smith, J. Jeff and Matthiadis, Anna and Strable, Josh and Kestell, Caitlin and Smith, William A.}, year={2023}, month={Sep} }
 @article{roche_montague_wang_dickey_ruiz-lambides_brent_platt_horvath_2023, title={Yearly variation coupled with social interactions shape the skin microbiome in free-ranging rhesus macaques}, volume={11}, ISSN={["2165-0497"]}, DOI={10.1128/spectrum.02974-23}, abstractNote={ABSTRACT}, number={5}, journal={MICROBIOLOGY SPECTRUM}, author={Roche, Christina E. and Montague, Michael J. and Wang, JiCi and Dickey, Allison N. and Ruiz-Lambides, Angelina and Brent, Lauren J. N. and Platt, Michael L. and Horvath, Julie E.}, year={2023} }
 @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={0888-7543}, url={http://dx.doi.org/10.1016/j.ygeno.2021.10.003}, 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}, publisher={Elsevier BV}, 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}, abstractNote={Of the 12 full-length feline leukocyte antigen class I (FLAI) loci, 3 are presumed to be classical: FLAI-E, FLAI-H, and FLAI-K. As diversity is a class Ia hallmark, multi-allelism is an important surrogate supporting a classical designation, in the absence of direct demonstration of T-cell restriction. Conversely, limited polymorphism at an expressed locus suggests regulation of immune effectors with invariant receptors, and non-classical status. FLAI-A, FLAI-J, FLAI-L, and FLAI-O are putative class Ib genes in cats. For both classes, identifying prevalent variants across outbred populations can illuminate specific genotypes to be prioritized for immune studies, as shared alleles direct shared responses. Since variation is concentrated in exons 2 and 3, which encode the antigen-binding domains, partial-length cloning/sequencing can be used for allele discovery, but is laborious and occasionally ambiguous. Here we develop a targeted approach to FLAI genotyping, using the single-molecule real-time (SMRT) platform, which allows full-length (3.4-kb) reads without assembly. Consensus sequences matched full-length Sanger references. Thirty-one new class Ia genes were found in 17 cats. Alleles segregated strongly by loci, and the origins of formerly difficult-to-assign sequences were resolved. Although not targeted, FLAI-L and FLAI-J, and the pseudogene FLAI-F, were also returned. Eighteen class Ib alleles were identified. Diversity was restricted and outside hypervariable regions. Both class Ib genes were transcriptionally active. Novel alternative splicing of FLAI-L was observed. SMRT sequencing of FLAI amplicons is useful for full-length genotyping at feline class Ia loci. High-throughput sequencing could allow highly accurate allele surveys in large cat cohorts.}, 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{perez-diaz_hayes_medina_webber_butz_dickey_lu_azcarate-peril_2019, title={Assessment of the non-lactic acid bacteria microbiota in fresh cucumbers and commercially fermented cucumber pickles brined with 6% NaCl}, volume={77}, ISSN={["1095-9998"]}, DOI={10.1016/j.fm.2018.08.003}, abstractNote={Limited documentation of the cucumber fermentation microbiome has impeded the understanding of the role of microbes on the quality of finished products. We characterized the microbiome of fresh and fermented cucumber samples using culture dependent and independent techniques, with an emphasis on the non-lactic acid bacteria (non-LAB) population. Insubstantial microbiome variations were observed among fresh cucumber types with Rhizobium (31.04%), Pseudomonas (14.08%), Pantoea (9.25%), Stenotrophomonas (6.83%), and Acinetobacter (6.5%) prevailing. The relative abundance of LAB remained below 0.4% and 4.0% on fresh cucumbers and day 3 of the fermentations brined with 6% sodium chloride, respectively. Fermentation cover brine samples collected on day 1 harbored Pseudomonas, Pantoea, Stenotrophomonas, Acinetobacter, Comamonas, Wautersiella, Microbacterium, Flavobacterium, Ochrobactrum and the Enterobacteriaceae, Citrobacter, Enterobacter and Kluyvera. Plate counts for presumptive Klebsiella and Pseudomonas from fermentation cover brine samples reached 2.80 ± 0.36 and 2.78 ± 0.83 log of CFU/mL, respectively, in 30% and 60% of the nine tanks scrutinized with selective media. Both genera were found in cover brine samples with pH values at 4.04 ± 0.15. We aim at elucidating whether the low relative abundance of non-LAB in commercial cucumber fermentations, in particular Pseudomonas and Enterobacteriaceae, impacts the quality of fermented cucumbers.}, journal={FOOD MICROBIOLOGY}, author={Perez-Diaz, Ilenys M. and Hayes, Janet S. and Medina, Eduardo and Webber, Ashlee M. and Butz, Natasha and Dickey, Allison N. and Lu, Zhongjing and Azcarate-Peril, Maria A.}, year={2019}, month={Feb}, pages={10–20} }
 @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{reinhart_motsinger-reif_dickey_yale_trepanier_2016, title={Genome-wide association study in immunocompetent patients with delayed hypersensitivity to sulfonamide antimicrobials}, volume={11}, number={6}, journal={PLoS One}, author={Reinhart, J. M. and Motsinger-Reif, A. and Dickey, A. and Yale, S. and Trepanier, L. A.}, year={2016} }