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2. Publisher Correction: The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control

Author

Olafson, Pia U, Aksoy, Serap, Attardo, Geoffrey M, Buckmeier, Greta, Chen, Xiaoting, Coates, Craig J, Davis, Megan, Dykema, Justin, Emrich, Scott J, Friedrich, Markus, Holmes, Christopher J, Ioannidis, Panagiotis, Jansen, Evan N, Jennings, Emily C, Lawson, Daniel, Martinson, Ellen O, Maslen, Gareth L, Meisel, Richard P, Murphy, Terence D, Nayduch, Dana, Nelson, David R, Oyen, Kennan J, Raszick, Tyler J, Ribeiro, José MC, Robertson, Hugh M, Rosendale, Andrew J, Sackton, Timothy B, Saelao, Perot, Swiger, Sonja L, Sze, Sing-Hoi, Tarone, Aaron M, Taylor, David B, Warren, Wesley C, Waterhouse, Robert M, Weirauch, Matthew T, Werren, John H, Wilson, Richard K, Zdobnov, Evgeny M, and Benoit, Joshua B

Subjects
Microbiology, Biological Sciences, Developmental Biology, Biological sciences
Abstract

Following publication of the original article [1], it was reported that the article copyright was incorrect. The correct copyright statement is: © This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2021. The original article [1] has been corrected.

Published
2021

3. The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control.

Author

Olafson, Pia U, Aksoy, Serap, Attardo, Geoffrey M, Buckmeier, Greta, Chen, Xiaoting, Coates, Craig J, Davis, Megan, Dykema, Justin, Emrich, Scott J, Friedrich, Markus, Holmes, Christopher J, Ioannidis, Panagiotis, Jansen, Evan N, Jennings, Emily C, Lawson, Daniel, Martinson, Ellen O, Maslen, Gareth L, Meisel, Richard P, Murphy, Terence D, Nayduch, Dana, Nelson, David R, Oyen, Kennan J, Raszick, Tyler J, Ribeiro, José MC, Robertson, Hugh M, Rosendale, Andrew J, Sackton, Timothy B, Saelao, Perot, Swiger, Sonja L, Sze, Sing-Hoi, Tarone, Aaron M, Taylor, David B, Warren, Wesley C, Waterhouse, Robert M, Weirauch, Matthew T, Werren, John H, Wilson, Richard K, Zdobnov, Evgeny M, and Benoit, Joshua B

Subjects
Chemoreceptor genes, Gene regulation, Insect adaptation, Insect immunity, Insect orthology, Metabolic detoxification genes, Muscid genomics, Opsin gene duplication, Stable fly genome, Biological Sciences, Developmental Biology
Abstract

BackgroundThe stable fly, Stomoxys calcitrans, is a major blood-feeding pest of livestock that has near worldwide distribution, causing an annual cost of over $2 billion for control and product loss in the USA alone. Control of these flies has been limited to increased sanitary management practices and insecticide application for suppressing larval stages. Few genetic and molecular resources are available to help in developing novel methods for controlling stable flies.ResultsThis study examines stable fly biology by utilizing a combination of high-quality genome sequencing and RNA-Seq analyses targeting multiple developmental stages and tissues. In conjunction, 1600 genes were manually curated to characterize genetic features related to stable fly reproduction, vector host interactions, host-microbe dynamics, and putative targets for control. Most notable was characterization of genes associated with reproduction and identification of expanded gene families with functional associations to vision, chemosensation, immunity, and metabolic detoxification pathways.ConclusionsThe combined sequencing, assembly, and curation of the male stable fly genome followed by RNA-Seq and downstream analyses provide insights necessary to understand the biology of this important pest. These resources and new data will provide the groundwork for expanding the tools available to control stable fly infestations. The close relationship of Stomoxys to other blood-feeding (horn flies and Glossina) and non-blood-feeding flies (house flies, medflies, Drosophila) will facilitate understanding of the evolutionary processes associated with development of blood feeding among the Cyclorrhapha.

Published
2021

6. No Evidence of SARS-CoV-2 Among Flies or Cockroaches in Households Where COVID-19 Positive Cases Resided

Author

Roundy, Christopher M, primary, Hamer, Sarah A, additional, Zecca, Italo B, additional, Davila, Edward B, additional, Auckland, Lisa D, additional, Tang, Wendy, additional, Gavranovic, Haley, additional, Swiger, Sonja L, additional, Tomberlin, Jeffery K, additional, Fischer, Rebecca S B, additional, Pauvolid-Corrêa, Alex, additional, and Hamer, Gabriel L, additional

Published
2022
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7. No Evidence of SARS-CoV-2 Among Flies or Cockroaches in COVID-19 Positive Households

Author

Roundy, Christopher M, primary, Hamer, Sarah A., additional, Zecca, Italo B., additional, Davila, Edward B., additional, Auckland, Lisa D., additional, Tang, Wendy, additional, Gavranovic, Haley, additional, Swiger, Sonja L., additional, Tomberlin, Jeffrey K., additional, Fischer, Rebecca S. B., additional, Pauvolid-Corrêa, Alex, additional, and Hamer, Gabriel L., additional

Published
2021
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8. The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control

Author

Olafson, Pia U., Aksoy, Serap, Attardo, Geoffrey M., Buckmeier, Greta, Chen, Xiaoting, Coates, Craig J., Davis, Megan, Dykema, Justin, Emrich, Scott J., Friedrich, Markus, Holmes, Christopher J., Ioannidis, Panagiotis, Jansen, Evan N., Jennings, Emily C., Lawson, Daniel, Martinson, Ellen O., Maslen, Gareth L., Meisel, Richard P., Murphy, Terence D., Nayduch, Dana, Nelson, David R., Oyen, Kennan J., Raszick, Tyler J., Ribeiro, José M.C., Robertson, Hugh M., Rosendale, Andrew J., Sackton, Timothy B., Saelao, Perot, Swiger, Sonja L., Sze, Sing Hoi, Tarone, Aaron M., Taylor, David B., Warren, Wesley C., Waterhouse, Robert M., Weirauch, Matthew T., Werren, John H., Wilson, Richard K., Zdobnov, Evgeny M., Benoit, Joshua B., Olafson, Pia U., Aksoy, Serap, Attardo, Geoffrey M., Buckmeier, Greta, Chen, Xiaoting, Coates, Craig J., Davis, Megan, Dykema, Justin, Emrich, Scott J., Friedrich, Markus, Holmes, Christopher J., Ioannidis, Panagiotis, Jansen, Evan N., Jennings, Emily C., Lawson, Daniel, Martinson, Ellen O., Maslen, Gareth L., Meisel, Richard P., Murphy, Terence D., Nayduch, Dana, Nelson, David R., Oyen, Kennan J., Raszick, Tyler J., Ribeiro, José M.C., Robertson, Hugh M., Rosendale, Andrew J., Sackton, Timothy B., Saelao, Perot, Swiger, Sonja L., Sze, Sing Hoi, Tarone, Aaron M., Taylor, David B., Warren, Wesley C., Waterhouse, Robert M., Weirauch, Matthew T., Werren, John H., Wilson, Richard K., Zdobnov, Evgeny M., and Benoit, Joshua B.

Abstract

Background: The stable fly, Stomoxys calcitrans, is a major blood-feeding pest of livestock that has near worldwide distribution, causing an annual cost of over $2 billion for control and product loss in the USA alone. Control of these flies has been limited to increased sanitary management practices and insecticide application for suppressing larval stages. Few genetic and molecular resources are available to help in developing novel methods for controlling stable flies. Results: This study examines stable fly biology by utilizing a combination of high-quality genome sequencing and RNA-Seq analyses targeting multiple developmental stages and tissues. In conjunction, 1600 genes were manually curated to characterize genetic features related to stable fly reproduction, vector host interactions, host-microbe dynamics, and putative targets for control. Most notable was characterization of genes associated with reproduction and identification of expanded gene families with functional associations to vision, chemosensation, immunity, and metabolic detoxification pathways. Conclusions: The combined sequencing, assembly, and curation of the male stable fly genome followed by RNA-Seq and downstream analyses provide insights necessary to understand the biology of this important pest. These resources and new data will provide the groundwork for expanding the tools available to control stable fly infestations. The close relationship of Stomoxys to other blood-feeding (horn flies and Glossina) and non-blood-feeding flies (house flies, medflies, Drosophila) will facilitate understanding of the evolutionary processes associated with development of blood feeding among the Cyclorrhapha.

Published
2021

9. Publisher Correction: The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control (BMC Biology, (2021), 19, 1, (41), 10.1186/s12915-021-00975-9)

Author

Olafson, Pia U., Aksoy, Serap, Attardo, Geoffrey M., Buckmeier, Greta, Chen, Xiaoting, Coates, Craig J., Davis, Megan, Dykema, Justin, Emrich, Scott J., Friedrich, Markus, Holmes, Christopher J., Ioannidis, Panagiotis, Jansen, Evan N., Jennings, Emily C., Lawson, Daniel, Martinson, Ellen O., Maslen, Gareth L., Meisel, Richard P., Murphy, Terence D., Nayduch, Dana, Nelson, David R., Oyen, Kennan J., Raszick, Tyler J., Ribeiro, José M.C., Robertson, Hugh M., Rosendale, Andrew J., Sackton, Timothy B., Saelao, Perot, Swiger, Sonja L., Sze, Sing Hoi, Tarone, Aaron M., Taylor, David B., Warren, Wesley C., Waterhouse, Robert M., Weirauch, Matthew T., Werren, John H., Wilson, Richard K., Zdobnov, Evgeny M., Benoit, Joshua B., Olafson, Pia U., Aksoy, Serap, Attardo, Geoffrey M., Buckmeier, Greta, Chen, Xiaoting, Coates, Craig J., Davis, Megan, Dykema, Justin, Emrich, Scott J., Friedrich, Markus, Holmes, Christopher J., Ioannidis, Panagiotis, Jansen, Evan N., Jennings, Emily C., Lawson, Daniel, Martinson, Ellen O., Maslen, Gareth L., Meisel, Richard P., Murphy, Terence D., Nayduch, Dana, Nelson, David R., Oyen, Kennan J., Raszick, Tyler J., Ribeiro, José M.C., Robertson, Hugh M., Rosendale, Andrew J., Sackton, Timothy B., Saelao, Perot, Swiger, Sonja L., Sze, Sing Hoi, Tarone, Aaron M., Taylor, David B., Warren, Wesley C., Waterhouse, Robert M., Weirauch, Matthew T., Werren, John H., Wilson, Richard K., Zdobnov, Evgeny M., and Benoit, Joshua B.

Abstract

Following publication of the original article [1], it was reported that the article copyright was incorrect. The correct copyright statement is: © This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2021. The original article [1] has been corrected.

Published
2021

10. Functional genomics of the stable fly,Stomoxys calcitrans, reveals mechanisms underlying reproduction, host interactions, and novel targets for pest control

Author

Olafson, Pia U., primary, Aksoy, Serap, additional, Attardo, Geoffrey M., additional, Buckmeier, Greta, additional, Chen, Xiaoting, additional, Coates, Craig J., additional, Davis, Megan, additional, Dykema, Justin, additional, Emrich, Scott J., additional, Friedrich, Markus, additional, Holmes, Christopher J., additional, Ioannidis, Panagiotis, additional, Jansen, Evan N., additional, Jennings, Emily C., additional, Lawson, Daniel, additional, Martinson, Ellen O., additional, Maslen, Gareth L., additional, Meisel, Richard P., additional, Murphy, Terence D., additional, Nayduch, Dana, additional, Nelson, David R., additional, Oyen, Kennan J., additional, Raszick, Tyler J., additional, Ribeiro, José M. C., additional, Robertson, Hugh M., additional, Rosendale, Andrew J., additional, Sackton, Timothy B., additional, Swiger, Sonja L., additional, Sze, Sing-Hoi, additional, Tarone, Aaron M., additional, Taylor, David B., additional, Warren, Wesley C., additional, Waterhouse, Robert M., additional, Weirauch, Matthew T., additional, Werren, John H., additional, Wilson, Richard K., additional, Zdobnov, Evgeny M., additional, and Benoit, Joshua B., additional

Published
2019
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11. Distribution of Culex coronator in Texas

Author

Sames, William J., primary, Dacko, Nina M., additional, Bolling, Bethany G., additional, Bosworth, Anthony B., additional, Swiger, Sonja L., additional, Duhrkopf, R. E., additional, and Burton, Roy G., additional

Published
2019
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14. Susceptibility of Alphitobius diaperinus in Texas to permethrin- and β-cyfluthrin-treated surfaces.

Author

Lyons, Brandon N, Crippen, Tawni L, Zheng, Le, Teel, Pete D, Swiger, Sonja L, and Tomberlin, Jeffery K

Subjects
INSECT pest control, ALPHITOBIUS diaperinus, PERMETHRIN, MEAL worms, BEETLES, INSECTICIDE application, HOST plants
Abstract

BACKGROUND Effective control of the lesser mealworm beetle, Alphitobius diaperinus, relies heavily on insecticides. The susceptibility level of beetles to these insecticides can be dependent on active ingredient, population treated, formulation, surface treated and timing of observation. The susceptibility of adult beetles from six populations to β-cyfluthrin was determined up to 48 h after exposure. The susceptibility of adult beetles to the label rate of β-cyfluthrin and permethrin formulations on concrete, wood-chip-type particle board and pressure-treated wood was determined up to 48 h post-exposure. RESULTS Variation in LC50 values at 2 and 24 h was found within and between beetle populations from two regions of Texas. The permethrin formulation had lower mean mortality than the β-cyfluthrin formulation on all surfaces tested. The permethrin formulation had high levels of recovery on all surfaces tested after 2 h. Surface affected the efficacy of the insecticides tested on killing adult beetles. CONCLUSION Permethrin-based insecticide had lower knockdown and persistence on various surfaces over time than β-cyfluthrin-based insecticide. Beetle recovery in less susceptible populations may necessitate longer observation periods for efficacy evaluations. Our study also shows that surfaces chosen can affect the efficacy of the compound on killing adult beetles. © 2016 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

Published
2017
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15. Additional file 1 of The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control

Author

Olafson, Pia U., Aksoy, Serap, Attardo, Geoffrey M., Buckmeier, Greta, Xiaoting Chen, Coates, Craig J., Davis, Megan, Dykema, Justin, Emrich, Scott J., Friedrich, Markus, Holmes, Christopher J., Ioannidis, Panagiotis, Jansen, Evan N., Jennings, Emily C., Lawson, Daniel, Martinson, Ellen O., Maslen, Gareth L., Meisel, Richard P., Murphy, Terence D., Nayduch, Dana, Nelson, David R., Oyen, Kennan J., Raszick, Tyler J., Ribeiro, José M. C., Robertson, Hugh M., Rosendale, Andrew J., Sackton, Timothy B., Perot Saelao, Swiger, Sonja L., Sing-Hoi Sze, Tarone, Aaron M., Taylor, David B., Warren, Wesley C., Waterhouse, Robert M., Weirauch, Matthew T., Werren, John H., Wilson, Richard K., Zdobnov, Evgeny M., and Benoit, Joshua B.

Subjects
2. Zero hunger
Abstract

Additional file 1: Main supplementary text file, including supplementary Tables S1-S12 and supplementary Figures S1-S21; Table S1. RNA-Sequencing and Whole Genome Sequencing Accession Numbers and Statistics. Table S2. Summary of Dfam repeat elements with > 1000 copies including number of unique elements for each family of elements and total number of genomic copies for each family. Table S3. Detailed list of repeat elements with total genomic copy number > 1000. Table S4. Autophagy genes identified from the Stomoxys genome. Table S5. Validation of Stomoxys transcript expression by RT-qPCR. Table S6. Bacterial contaminating scaffolds located in the Stomoxys genome assembly. Table S7. Predicted lateral gene transfer events identified from the Stomoxys genome. Table S8. Components of the immune deficiency, Toll, and JAK/STAT pathways identified from the Stomoxys genome. Table S9. Manually annotated Stomoxys immune system gene family members. Table S10. RNA-Seq normalized expression values for transcripts annotated as antimicrobial peptides. Table S11. Stomoxys opsin gene compilation. Table S12. Aquaporin gene names and corresponding symbols, model numbers, scaffolds, and arthropod homologues. Figure S1. Phylogenetic placement and genomic comparisons for Stomoxys calcitrans and other fly species. Figure S2. Pearson's correlation of RNA-Seq and RT-qPCR results. Figure S3. Average read depth across predicted lateral gene transfer candidates. Figure S4. Stomoxys calcitrans genomic scaffold housing 11 defensin gene models. Figure S5. Maximum likelihood phylogenetic tree of PGRP protein sequences from S. calcitrans (red), M. domestica (black), and D. melanogaster (blue). Figure S6. Alignment of Stomoxys PGRP-S sequences with characterized D. melanogaster PGRP-SC1 (C0HK98) and –SC2 (Q9VX2) and N-acetylmuramoyl-L-alanine amidase (P00806). Figure S7. Alignment of Stomoxys PGRP-L sequences with characterized D. melanogaster PGRP-L proteins and N-acetylmuramoyl-L-alanine amidase. Figure S8. Stomoxys calcitrans Odorant Binding Protein Gene Family. Figure S9. Duplicated OS-E-like and an OS-X ortholog in Stomoxys and Musca. Figure S10. Stomoxys calcitrans Odorant Receptor Gene Family. Figure S11. Stomoxys calcitrans Gustatory Receptor Gene Family. Figure S12. Stomoxys calcitrans Ionotropic Receptor Gene Family. Figure S13. Maximum likelihood tree of dipteran opsin gene relationships. Figure S14. Phylogenetic analysis of the Stomoxys Rh1 gene cluster and Genomic organization and evolution of the S. calcitrans Rh1 opsin subfamily. Figure S15. Analysis of tuning site 17 variation in Stomoxys and Musca Rh1 paralogs. Figure S16, S18, S19. Phylogenetic relationship of catalytic carboxyesterases (S16), glutathione-S-transferases (S18), and Cys-Loop Ligand Gated Ion Channels (S19) from Stomoxys relative to Musca and Drosophila. Figure S17. Phylogenetic analysis of carboxylesterases with a role in neuronal development. Figure S20. Cytochrome P450 (CYP450) genes clustered on Stomoxys scaffolds and evidence for expansions in muscids relative to Drosophila. Figure S21. Phylogenetic analysis of cytochrome P450 genes from Stomoxys calcitrans.

16. Additional file 1 of The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control

Author

Olafson, Pia U., Aksoy, Serap, Attardo, Geoffrey M., Buckmeier, Greta, Xiaoting Chen, Coates, Craig J., Davis, Megan, Dykema, Justin, Emrich, Scott J., Friedrich, Markus, Holmes, Christopher J., Ioannidis, Panagiotis, Jansen, Evan N., Jennings, Emily C., Lawson, Daniel, Martinson, Ellen O., Maslen, Gareth L., Meisel, Richard P., Murphy, Terence D., Nayduch, Dana, Nelson, David R., Oyen, Kennan J., Raszick, Tyler J., Ribeiro, José M. C., Robertson, Hugh M., Rosendale, Andrew J., Sackton, Timothy B., Perot Saelao, Swiger, Sonja L., Sing-Hoi Sze, Tarone, Aaron M., Taylor, David B., Warren, Wesley C., Waterhouse, Robert M., Weirauch, Matthew T., Werren, John H., Wilson, Richard K., Zdobnov, Evgeny M., and Benoit, Joshua B.

Subjects
2. Zero hunger
Abstract

Additional file 1: Main supplementary text file, including supplementary Tables S1-S12 and supplementary Figures S1-S21; Table S1. RNA-Sequencing and Whole Genome Sequencing Accession Numbers and Statistics. Table S2. Summary of Dfam repeat elements with > 1000 copies including number of unique elements for each family of elements and total number of genomic copies for each family. Table S3. Detailed list of repeat elements with total genomic copy number > 1000. Table S4. Autophagy genes identified from the Stomoxys genome. Table S5. Validation of Stomoxys transcript expression by RT-qPCR. Table S6. Bacterial contaminating scaffolds located in the Stomoxys genome assembly. Table S7. Predicted lateral gene transfer events identified from the Stomoxys genome. Table S8. Components of the immune deficiency, Toll, and JAK/STAT pathways identified from the Stomoxys genome. Table S9. Manually annotated Stomoxys immune system gene family members. Table S10. RNA-Seq normalized expression values for transcripts annotated as antimicrobial peptides. Table S11. Stomoxys opsin gene compilation. Table S12. Aquaporin gene names and corresponding symbols, model numbers, scaffolds, and arthropod homologues. Figure S1. Phylogenetic placement and genomic comparisons for Stomoxys calcitrans and other fly species. Figure S2. Pearson's correlation of RNA-Seq and RT-qPCR results. Figure S3. Average read depth across predicted lateral gene transfer candidates. Figure S4. Stomoxys calcitrans genomic scaffold housing 11 defensin gene models. Figure S5. Maximum likelihood phylogenetic tree of PGRP protein sequences from S. calcitrans (red), M. domestica (black), and D. melanogaster (blue). Figure S6. Alignment of Stomoxys PGRP-S sequences with characterized D. melanogaster PGRP-SC1 (C0HK98) and –SC2 (Q9VX2) and N-acetylmuramoyl-L-alanine amidase (P00806). Figure S7. Alignment of Stomoxys PGRP-L sequences with characterized D. melanogaster PGRP-L proteins and N-acetylmuramoyl-L-alanine amidase. Figure S8. Stomoxys calcitrans Odorant Binding Protein Gene Family. Figure S9. Duplicated OS-E-like and an OS-X ortholog in Stomoxys and Musca. Figure S10. Stomoxys calcitrans Odorant Receptor Gene Family. Figure S11. Stomoxys calcitrans Gustatory Receptor Gene Family. Figure S12. Stomoxys calcitrans Ionotropic Receptor Gene Family. Figure S13. Maximum likelihood tree of dipteran opsin gene relationships. Figure S14. Phylogenetic analysis of the Stomoxys Rh1 gene cluster and Genomic organization and evolution of the S. calcitrans Rh1 opsin subfamily. Figure S15. Analysis of tuning site 17 variation in Stomoxys and Musca Rh1 paralogs. Figure S16, S18, S19. Phylogenetic relationship of catalytic carboxyesterases (S16), glutathione-S-transferases (S18), and Cys-Loop Ligand Gated Ion Channels (S19) from Stomoxys relative to Musca and Drosophila. Figure S17. Phylogenetic analysis of carboxylesterases with a role in neuronal development. Figure S20. Cytochrome P450 (CYP450) genes clustered on Stomoxys scaffolds and evidence for expansions in muscids relative to Drosophila. Figure S21. Phylogenetic analysis of cytochrome P450 genes from Stomoxys calcitrans.

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