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2. Correction to: Genome-enabled insights into the biology of thrips as crop pests

Author

Rotenberg, Dorith, Baumann, Aaron A, Ben-Mahmoud, Sulley, Christiaens, Olivier, Dermauw, Wannes, Ioannidis, Panagiotis, Jacobs, Chris GC, Vargas Jentzsch, Iris M, Oliver, Jonathan E, Poelchau, Monica F, Rajarapu, Swapna Priya, Schneweis, Derek J, Snoeck, Simon, Taning, Clauvis NT, Wei, Dong, Widana Gamage, Shirani MK, Hughes, Daniel ST, Murali, Shwetha C, Bailey, Samuel T, Bejerman, Nicolas E, Holmes, Christopher J, Jennings, Emily C, Rosendale, Andrew J, Rosselot, Andrew, Hervey, Kaylee, Schneweis, Brandi A, Cheng, Sammy, Childers, Christopher, Simão, Felipe A, Dietzgen, Ralf G, Chao, Hsu, Dinh, Huyen, Doddapaneni, Harsha Vardhan, Dugan, Shannon, Han, Yi, Lee, Sandra L, Muzny, Donna M, Qu, Jiaxin, Worley, Kim C, Benoit, Joshua B, Friedrich, Markus, Jones, Jeffery W, Panfilio, Kristen A, Park, Yoonseong, Robertson, Hugh M, Smagghe, Guy, Ullman, Diane E, van der Zee, Maurijn, Van Leeuwen, Thomas, Veenstra, Jan A, Waterhouse, Robert M, Weirauch, Matthew T, Werren, John H, Whitfield, Anna E, Zdobnov, Evgeny M, Gibbs, Richard A, and Richards, Stephen

Subjects
Biological Sciences, Developmental Biology, Biological sciences
Abstract

An amendment to this paper has been published and can be accessed via the original article.

Published
2020

3. Genome-enabled insights into the biology of thrips as crop pests

Author

Rotenberg, Dorith, Baumann, Aaron A, Ben-Mahmoud, Sulley, Christiaens, Olivier, Dermauw, Wannes, Ioannidis, Panagiotis, Jacobs, Chris GC, Vargas Jentzsch, Iris M, Oliver, Jonathan E, Poelchau, Monica F, Rajarapu, Swapna Priya, Schneweis, Derek J, Snoeck, Simon, Taning, Clauvis NT, Wei, Dong, Widana Gamage, Shirani MK, Hughes, Daniel ST, Murali, Shwetha C, Bailey, Samuel T, Bejerman, Nicolas E, Holmes, Christopher J, Jennings, Emily C, Rosendale, Andrew J, Rosselot, Andrew, Hervey, Kaylee, Schneweis, Brandi A, Cheng, Sammy, Childers, Christopher, Simão, Felipe A, Dietzgen, Ralf G, Chao, Hsu, Dinh, Huyen, Doddapaneni, Harsha Vardhan, Dugan, Shannon, Han, Yi, Lee, Sandra L, Muzny, Donna M, Qu, Jiaxin, Worley, Kim C, Benoit, Joshua B, Friedrich, Markus, Jones, Jeffery W, Panfilio, Kristen A, Park, Yoonseong, Robertson, Hugh M, Smagghe, Guy, Ullman, Diane E, van der Zee, Maurijn, Van Leeuwen, Thomas, Veenstra, Jan A, Waterhouse, Robert M, Weirauch, Matthew T, Werren, John H, Whitfield, Anna E, Zdobnov, Evgeny M, Gibbs, Richard A, and Richards, Stephen

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, Animals, Crops, Agricultural, Feeding Behavior, Food Chain, Genome, Insect, Immunity, Innate, Life History Traits, Perception, Phylogeny, Reproduction, Thysanoptera, Transcriptome, Western flower thrips, Hemipteroid assemblage, Insect genomics, Tospovirus, Salivary glands, Chemosensory receptors, Opsins, Detoxification, Innate immunity, Developmental Biology, Biological sciences
Abstract

BackgroundThe western flower thrips, Frankliniella occidentalis (Pergande), is a globally invasive pest and plant virus vector on a wide array of food, fiber, and ornamental crops. The underlying genetic mechanisms of the processes governing thrips pest and vector biology, feeding behaviors, ecology, and insecticide resistance are largely unknown. To address this gap, we present the F. occidentalis draft genome assembly and official gene set.ResultsWe report on the first genome sequence for any member of the insect order Thysanoptera. Benchmarking Universal Single-Copy Ortholog (BUSCO) assessments of the genome assembly (size = 415.8 Mb, scaffold N50 = 948.9 kb) revealed a relatively complete and well-annotated assembly in comparison to other insect genomes. The genome is unusually GC-rich (50%) compared to other insect genomes to date. The official gene set (OGS v1.0) contains 16,859 genes, of which ~ 10% were manually verified and corrected by our consortium. We focused on manual annotation, phylogenetic, and expression evidence analyses for gene sets centered on primary themes in the life histories and activities of plant-colonizing insects. Highlights include the following: (1) divergent clades and large expansions in genes associated with environmental sensing (chemosensory receptors) and detoxification (CYP4, CYP6, and CCE enzymes) of substances encountered in agricultural environments; (2) a comprehensive set of salivary gland genes supported by enriched expression; (3) apparent absence of members of the IMD innate immune defense pathway; and (4) developmental- and sex-specific expression analyses of genes associated with progression from larvae to adulthood through neometaboly, a distinct form of maturation differing from either incomplete or complete metamorphosis in the Insecta.ConclusionsAnalysis of the F. occidentalis genome offers insights into the polyphagous behavior of this insect pest that finds, colonizes, and survives on a widely diverse array of plants. The genomic resources presented here enable a more complete analysis of insect evolution and biology, providing a missing taxon for contemporary insect genomics-based analyses. Our study also offers a genomic benchmark for molecular and evolutionary investigations of other Thysanoptera species.

Published
2020

6. Drosophila Glue Expulsion and Spreading Behavior is Modulated by Neuropeptidergic Mip-SPR Signaling from a Descending Command Neuron

Author

Fernandez-Acosta, Magdalena, primary, Zanini, Rebeca, additional, Heredia, Fabiana, additional, Volonte, Yanel, additional, Menezes, Juliane, additional, Pruger, Katja, additional, Ibarra, Julieta, additional, Arana, Maite, additional, Perez, Maria Sol, additional, Veenstra, Jan A, additional, Wegener, Christian, additional, Gontijo, Alisson M., additional, and Garelli, Andres, additional

Published
2024
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15. Effectiveness and cost-effectiveness of a nurse-delivered intervention to improve adherence to treatment for HIV: a pragmatic, multicentre, open-label, randomised clinical trial

Author

de Bruin, Marijn, Oberjé, Edwin J M, Viechtbauer, Wolfgang, Nobel, Hans-Erik, Hiligsmann, Mickaël, van Nieuwkoop, Cees, Veenstra, Jan, Pijnappel, Frank J, Kroon, Frank P, van Zonneveld, Laura, Groeneveld, Paul H P, van Broekhuizen, Marjolein, Evers, Silvia M A A, and Prins, Jan M

Published
2017
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22. Positive impact of [18F]FDG-PET/CT on mortality in patients with Staphylococcus aureus bacteremia explained by immortal time bias

Author

Infection & Immunity, Epi Infectieziekten Team 1, JC onderzoeksprogramma Infectious Diseases, Epi Infectieziekten, Epidemiology of Sepsis & Inflammation in Critically Ill Patients, van der Vaart, Thomas W, Prins, Jan M, van Werkhoven, Cornelis H, Ten Doesschate, Thijs, Soetekouw, Robin, van Twillert, Gitte, Veenstra, Jan, Herpers, Bjorn L, Rozemeijer, Wouter, Jansen, Rogier R, Bonten, Marc J M, van der Meer, Jan T M, Infection & Immunity, Epi Infectieziekten Team 1, JC onderzoeksprogramma Infectious Diseases, Epi Infectieziekten, Epidemiology of Sepsis & Inflammation in Critically Ill Patients, van der Vaart, Thomas W, Prins, Jan M, van Werkhoven, Cornelis H, Ten Doesschate, Thijs, Soetekouw, Robin, van Twillert, Gitte, Veenstra, Jan, Herpers, Bjorn L, Rozemeijer, Wouter, Jansen, Rogier R, Bonten, Marc J M, and van der Meer, Jan T M

Published
2023

25. Positive Impact of [18F]FDG-PET/CT on Mortality in Patients With Staphylococcus aureus Bacteremia Explained by Immortal Time Bias

Author

van der Vaart, Thomas W, primary, Prins, Jan M, additional, van Werkhoven, Cornelis H, additional, ten Doesschate, Thijs, additional, Soetekouw, Robin, additional, van Twillert, Gitte, additional, Veenstra, Jan, additional, Herpers, Bjorn L, additional, Rozemeijer, Wouter, additional, Jansen, Rogier R, additional, Bonten, Marc J M, additional, and van der Meer, Jan T M, additional

Published
2023
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31. Aphid PDF alignment and supplementary Tables from Pigment-dispersing factor is present in circadian clock neurons of pea aphids and may mediate photoperiodic signalling to insulin-producing cells

Author

Colizzi, Francesca Sara, Veenstra, Jan A., Rezende, Gustavo L., Helfrich-Förster, Charlotte, and Martínez-Torres, David

Abstract

The neuropeptide pigment-dispersing factor (PDF) plays a pivotal role in the circadian clock of most Ecdysozoa and is additionally involved in the timing of seasonal responses of several photoperiodic species. The pea aphid, Acyrthosiphon pisum, is a paradigmatic photoperiodic species with an annual life cycle tightly coupled to the seasonal changes in day length. Nevertheless, PDF could not be identified in A. pisum so far. In the present study, we identified a PDF-coding gene that has undergone significant changes in the otherwise highly conserved insect C-terminal amino acid sequence. A newly generated aphid-specific PDF antibody stained four neurons in each hemisphere of the aphid brain that co-express the clock protein Period and have projections to the pars lateralis that are highly plastic and change their appearance in a daily and seasonal manner, resembling those of the fruit fly PDF neurons. Most intriguingly, the PDF terminals overlap with dendrites of the insulin-like peptide (ILP) positive neurosecretory cells in the pars intercerebralis and with putative terminals of Cryptochrome (CRY) positive clock neurons. Since ILP has been previously shown to be crucial for seasonal adaptations and CRY might serve as a circadian photoreceptor vital for measuring day length, our results suggest that PDF plays a critical role in aphid seasonal timing.

Published
2023
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35. Positive Impact of [18F]FDG-PET/CT on Mortality in Patients With Staphylococcus aureus Bacteremia Explained by Immortal Time Bias.

Author

Vaart, Thomas W van der, Prins, Jan M, Werkhoven, Cornelis H van, Doesschate, Thijs ten, Soetekouw, Robin, Twillert, Gitte van, Veenstra, Jan, Herpers, Bjorn L, Rozemeijer, Wouter, Jansen, Rogier R, Bonten, Marc J M, and Meer, Jan T M van der

Subjects
BACTEREMIA, RESEARCH, CAUSES of death, CONFIDENCE intervals, TIME, POSITRON emission tomography computed tomography, STAPHYLOCOCCAL diseases, TREATMENT effectiveness, RADIOPHARMACEUTICALS, POSITRON emission tomography, STAPHYLOCOCCUS aureus, UNIVERSITIES & colleges, DESCRIPTIVE statistics, DEOXY sugars, COMPUTED tomography, DATA analysis software, LONGITUDINAL method, PROPORTIONAL hazards models, DISEASE complications
Abstract

Background Several studies have suggested that in patients with Staphylococcus aureus bacteremia (SAB) [18F] fluorodeoxyglucose positron emission tomography/computed tomography ([18F]FDG-PET/CT) improves outcome. However, these studies often ignored possible immortal time bias. Methods Prospective multicenter cohort study in 2 university and 5 non-university hospitals, including all patients with SAB. [18F]FDG-PET/CT was performed on clinical indication as part of usual care. Primary outcome was 90-day all-cause mortality. Effect of [18F]FDG-PET/CT was modeled with a Cox proportional hazards model using [18F]FDG-PET/CT as a time-varying variable and corrected for confounders for mortality (age, Charlson score, positive follow-up cultures, septic shock, and endocarditis). Secondary outcome was 90-day infection-related mortality (assessed by adjudication committee) using the same analysis. In a subgroup-analysis, we determined the effect of [18F]FDG-PET/CT in patients with high risk of metastatic infection. Results Of 476 patients, 178 (37%) underwent [18F]FDG-PET/CT. Day-90 all-cause mortality was 31% (147 patients), and infection-related mortality was 17% (83 patients). The confounder adjusted hazard ratio (aHR) for all-cause mortality was 0.50 (95% confidence interval [CI]:.34–.74) in patients that underwent [18F]FDG-PET/CT. Adjustment for immortal time bias changed the aHR to 1.00 (95% CI.68–1.48). Likewise, after correction for immortal time bias, [18F]FDG-PET/CT had no effect on infection-related mortality (cause specific aHR 1.30 [95% CI.77–2.21]), on all-cause mortality in patients with high-risk SAB (aHR 1.07 (95% CI.63–1.83) or on infection-related mortality in high-risk SAB (aHR for 1.24 [95% CI.67–2.28]). Conclusions After adjustment for immortal time bias [18F]FDG-PET/CT was not associated with day-90 all-cause or infection-related mortality in patients with SAB. [ABSTRACT FROM AUTHOR]

Published
2023
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37. Prediction rules for ruling out endocarditis in patients with Staphylococcus aureus bacteremia

Author

Epi Infectieziekten Team 1, Infection & Immunity, JC onderzoeksprogramma Infectious Diseases, Epi Infectieziekten, van der Vaart, Thomas W, Prins, Jan M, Soetekouw, Robin, van Twillert, Gitte, Veenstra, Jan, Herpers, Bjorn L, Rozemeijer, Wouter, Jansen, Rogier R, Bonten, Marc J M, van der Meer, Jan T M, Epi Infectieziekten Team 1, Infection & Immunity, JC onderzoeksprogramma Infectious Diseases, Epi Infectieziekten, van der Vaart, Thomas W, Prins, Jan M, Soetekouw, Robin, van Twillert, Gitte, Veenstra, Jan, Herpers, Bjorn L, Rozemeijer, Wouter, Jansen, Rogier R, Bonten, Marc J M, and van der Meer, Jan T M

Published
2022

41. Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle

Author

Kirkness, Ewen F., Haas, Brian J., Sun, Weilin, Braig, Henk R., Perotti, M. Alejandra, Clark, John M., Lee, Si Hyeock, Robertson, Hugh M., Kennedy, Ryan C., Elhaik, Eran, Gerlach, Daniel, Kriventseva, Evgenia V., Elsik, Christine G., Graur, Dan, Hill, Catherine A., Veenstra, Jan A., Walenz, Brian, Tubío, José Manuel C., Ribeiro, José M. C., Rozas, Julio, Johnston, J. Spencer, Reese, Justin T., Popadic, Aleksandar, Tojo, Marta, Raoult, Didier, Reed, David L., Tomoyasu, Yoshinori, Krause, Emily, Mittapalli, Omprakash, Margam, Venu M., Li, Hong-Mei, Meyer, Jason M., Johnson, Reed M., Romero-Severson, Jeanne, VanZee, Janice Pagel, Alvarez-Ponce, David, Vieira, Filipe G., Aguadé, Montserrat, Guirao-Rico, Sara, Anzola, Juan M., Yoon, Kyong S., Strycharz, Joseph P., Unger, Maria F., Christley, Scott, Lobo, Neil F., Seufferheld, Manfredo J., Wang, NaiKuan, Dasch, Gregory A., Struchiner, Claudio J., Madey, Greg, Hannick, Linda I., Bidwell, Shelby, Joardar, Vinita, Caler, Elisabet, Shao, Renfu, Barker, Stephen C., Cameron, Stephen, Bruggner, Robert V., Regier, Allison, Johnson, Justin, Viswanathan, Lakshmi, Utterback, Terry R., Sutton, Granger G., Lawson, Daniel, Waterhouse, Robert M., Venter, J. Craig, Strausberg, Robert L., Berenbaum, May R., Collins, Frank H., Zdobnov, Evgeny M., and Pittendrigh, Barry R.

Published
2010

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