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1. Detection of chromosomal aneuploidy in ancient genomes

Author

Anastasiadou, Kyriaki, Silva, Marina, Booth, Thomas, Speidel, Leo, Audsley, Tony, Barrington, Christopher, Buckberry, Jo, Fernandes, Diana, Ford, Ben, Gibson, Mark, Gilardet, Alexandre, Glocke, Isabelle, Keefe, Katie, Kelly, Monica, Masters, Mackenzie, McCabe, Jesse, McIntyre, Lauren, Ponce, Paola, Rowland, Stephen, Ruiz Ventura, Jordi, Swali, Pooja, Tait, Frankie, Walker, David, Webb, Helen, Williams, Mia, Witkin, Annsofie, Holst, Malin, Loe, Louise, Armit, Ian, Schulting, Rick, and Skoglund, Pontus

Published
2024
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4. Transcriptome Complexities Across Eukaryotes

Author

Titus-McQuillan, James E., Nanni, Adalena V., McIntyre, Lauren M., and Rogers, Rebekah L.

Subjects
Quantitative Biology - Genomics
Abstract

Genomic complexity is a growing field of evolution, with case studies for comparative evolutionary analyses in model and emerging non-model systems. Understanding complexity and the functional components of the genome is an untapped wealth of knowledge ripe for exploration. With the "remarkable lack of correspondence" between genome size and complexity, there needs to be a way to quantify complexity across organisms. In this study we use a set of complexity metrics that allow for evaluation of changes in complexity using TranD. We ascertain if complexity is increasing or decreasing across transcriptomes and at what structural level, as complexity is varied. We define three metrics -- TpG, EpT, and EpG in this study to quantify the complexity of the transcriptome that encapsulate the dynamics of alternative splicing. Here we compare complexity metrics across 1) whole genome annotations, 2) a filtered subset of orthologs, and 3) novel genes to elucidate the impacts of ortholog and novel genes in transcriptome analysis. We also derive a metric from Hong et al., 2006, Effective Exon Number (EEN), to compare the distribution of exon sizes within transcripts against random expectations of uniform exon placement. EEN accounts for differences in exon size, which is important because novel genes differences in complexity for orthologs and whole transcriptome analyses are biased towards low complexity genes with few exons and few alternative transcripts. With our metric analyses, we are able to implement changes in complexity across diverse lineages with greater precision and accuracy than previous cross-species comparisons under ortholog conditioning. These analyses represent a step forward toward whole transcriptome analysis in the emerging field of non-model evolutionary genomics, with key insights for evolutionary inference of complexity changes on deep timescales across the tree of life. We suggest a means to quantify biases generated in ortholog calling and correct complexity analysis for lineage-specific effects. With these metrics, we directly assay the quantitative properties of newly formed lineage-specific genes as they lower complexity in transcriptomes., Comment: 33 pages main text; 6 main figures; 25 pages of supplement; 1 supplementary table; 24 Supp Figures; 58 pages total

Published
2022

5. The effect of the Katz parameter on node ranking, with a medical application

Author

Rehm, Hunter, Matar, Mona, Rombach, Puck, and McIntyre, Lauren

Subjects
Physics - Physics and Society, 68R10, 65F60
Abstract

Katz centrality is a popular network centrality measure. It takes a (weighted) count of all walks starting at each node, with an additional damping factor of $\alpha$ that tunes the influence of walks as lengths increase. We introduce a tool to compare different centrality measures in terms of their node rankings, which takes into account that a relative ranking of two nodes by a centrality measure is unreliable if their scores are within a margin of error of one another. We employ this tool to understand the effect of the $\alpha$-parameter on the lengths of walks that significantly affect the ranking of nodes. In particular, we find an upper bound on the lengths of the walks that determine the node ranking up to this margin of error. If an application imposes a realistic bound on possible walk lengths, this set of tools may be helpful to determine a suitable value for $\alpha$. We show the effect of $\alpha$ on rankings when applied to the Susceptibility Inference Network, which contains subject matter expert informed data that represents the probabilities of medical conditions progressing from one to another. This network is part of the Medical Extensible Dynamic Probabilistic Risk Assessment Tool, developed by NASA, an event-based risk modeling tool that assesses human health and medical risk during space exploration missions.

Published
2022

10. Uncovering hidden genetic variation in photosynthesis of field‐grown maize under ozone pollution

Author

Choquette, Nicole E, Ogut, Funda, Wertin, Timothy M, Montes, Christopher M, Sorgini, Crystal A, Morse, Alison M, Brown, Patrick J, Leakey, Andrew DB, McIntyre, Lauren M, and Ainsworth, Elizabeth A

Subjects
Genetics, Climate-Related Exposures and Conditions, Environmental Pollution, Genetic Variation, Ozone, Photosynthesis, Plant Leaves, Zea mays, FACE, air pollution, global climate change, heritability, maize, ozone, photosynthesis, Environmental Sciences, Biological Sciences, Ecology
Abstract

Ozone is the most damaging air pollutant to crops, currently reducing Midwest US maize production by up to 10%, yet there has been very little effort to adapt germplasm for ozone tolerance. Ozone enters plants through stomata, reacts to form reactive oxygen species in the apoplast and ultimately decreases photosynthetic C gain. In this study, 10 diverse inbred parents were crossed in a half-diallel design to create 45 F1 hybrids, which were tested for ozone response in the field using free air concentration enrichment (FACE). Ozone stress increased the heritability of photosynthetic traits and altered genetic correlations among traits. Hybrids from parents Hp301 and NC338 showed greater sensitivity to ozone stress, and disrupted relationships among photosynthetic traits. The physiological responses underlying sensitivity to ozone differed in hybrids from the two parents, suggesting multiple mechanisms of response to oxidative stress. FACE technology was essential to this evaluation because genetic variation in photosynthesis under elevated ozone was not predictable based on performance at ambient ozone. These findings suggest that selection under elevated ozone is needed to identify deleterious alleles in the world's largest commodity crop.

Published
2019

11. High-resolution methylome analysis uncovers stress-responsive genomic hotspots and drought-sensitive TE superfamilies in the clonal Lombardy poplar

Author

Peña-Ponton, Cristian, primary, Diez-Rodriguez, Barbara, additional, Perez-Bello, Paloma, additional, Becker, Claude, additional, McIntyre, Lauren M, additional, van der Putten, Wim H, additional, De Paoli, Emanuele, additional, Heer, Katrin, additional, Opgenoorth, Lars, additional, and Verhoeven, Koen J F, additional

Published
2024
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13. High-resolution methylome analysis uncovers stress-responsive genomic hotspots and drought-sensitive transposable element superfamilies in the clonal Lombardy poplar.

Author

Peña-Ponton, Cristian, Diez-Rodriguez, Barbara, Perez-Bello, Paloma, Becker, Claude, McIntyre, Lauren M, Putten, Wim H van der, Paoli, Emanuele De, Heer, Katrin, Opgenoorth, Lars, and Verhoeven, Koen J F

Subjects
DNA methylation, WHOLE genome sequencing, BLACK poplar, SALICYLIC acid, ABIOTIC stress, DEMETHYLATION
Abstract

DNA methylation is environment-sensitive and can mediate stress responses. In trees, changes in the environment might cumulatively shape the methylome landscape over time. However, because high-resolution methylome studies usually focus on single environmental cues, the stress-specificity and long-term stability of methylation responses remain unclear. Here, we studied the methylome plasticity of a Populus nigra cv. 'Italica' clone widely distributed across Europe. Adult trees from different geographic locations were clonally propagated in a common garden experiment and exposed to cold, heat, drought, herbivory, rust infection, and salicylic acid treatments. Whole-genome bisulfite sequencing revealed stress-induced and naturally occurring DNA methylation variants. In CG/CHG contexts, the same genomic regions were often affected by multiple stresses, suggesting a generic methylome response. Moreover, these variants showed striking overlap with naturally occurring methylation variants between trees from different locations. Drought treatment triggered CHH hypermethylation of transposable elements, affecting entire superfamilies near drought-responsive genes. Thus, we revealed genomic hotspots of methylation change that are not stress-specific and that contribute to natural DNA methylation variation, and identified stress-specific hypermethylation of entire transposon superfamilies with possible functional consequences. Our results underscore the importance of studying multiple stressors in a single experiment for recognizing general versus stress-specific methylome responses. [ABSTRACT FROM AUTHOR]

Published
2024
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14. Large-scale migration into Britain during the Middle to Late Bronze Age

Author

Patterson, Nick, Isakov, Michael, Booth, Thomas, Büster, Lindsey, Fischer, Claire-Elise, Olalde, Iñigo, Ringbauer, Harald, Akbari, Ali, Cheronet, Olivia, Bleasdale, Madeleine, Adamski, Nicole, Altena, Eveline, Bernardos, Rebecca, Brace, Selina, Broomandkhoshbacht, Nasreen, Callan, Kimberly, Candilio, Francesca, Culleton, Brendan, Curtis, Elizabeth, Demetz, Lea, Carlson, Kellie Sara Duffett, Edwards, Ceiridwen J., Fernandes, Daniel M., Foody, M. George B., Freilich, Suzanne, Goodchild, Helen, Kearns, Aisling, Lawson, Ann Marie, Lazaridis, Iosif, Mah, Matthew, Mallick, Swapan, Mandl, Kirsten, Micco, Adam, Michel, Megan, Morante, Guillermo Bravo, Oppenheimer, Jonas, Özdoğan, Kadir Toykan, Qiu, Lijun, Schattke, Constanze, Stewardson, Kristin, Workman, J. Noah, Zalzala, Fatma, Zhang, Zhao, Agustí, Bibiana, Allen, Tim, Almássy, Katalin, Amkreutz, Luc, Ash, Abigail, Baillif-Ducros, Christèle, Barclay, Alistair, Bartosiewicz, László, Baxter, Katherine, Bernert, Zsolt, Blažek, Jan, Bodružić, Mario, Boissinot, Philippe, Bonsall, Clive, Bradley, Pippa, Brittain, Marcus, Brookes, Alison, Brown, Fraser, Brown, Lisa, Brunning, Richard, Budd, Chelsea, Burmaz, Josip, Canet, Sylvain, Carnicero-Cáceres, Silvia, Čaušević-Bully, Morana, Chamberlain, Andrew, Chauvin, Sébastien, Clough, Sharon, Čondić, Natalija, Coppa, Alfredo, Craig, Oliver, Črešnar, Matija, Cummings, Vicki, Czifra, Szabolcs, Danielisová, Alžběta, Daniels, Robin, Davies, Alex, de Jersey, Philip, Deacon, Jody, Deminger, Csilla, Ditchfield, Peter W., Dizdar, Marko, Dobeš, Miroslav, Dobisíková, Miluše, Domboróczki, László, Drinkall, Gail, Đukić, Ana, Ernée, Michal, Evans, Christopher, Evans, Jane, Fernández-Götz, Manuel, Filipović, Slavica, Fitzpatrick, Andrew, Fokkens, Harry, Fowler, Chris, Fox, Allison, Gallina, Zsolt, Gamble, Michelle, González Morales, Manuel R., González-Rabanal, Borja, Green, Adrian, Gyenesei, Katalin, Habermehl, Diederick, Hajdu, Tamás, Hamilton, Derek, Harris, James, Hayden, Chris, Hendriks, Joep, Hernu, Bénédicte, Hey, Gill, Horňák, Milan, Ilon, Gábor, Istvánovits, Eszter, Jones, Andy M., Kavur, Martina Blečić, Kazek, Kevin, Kenyon, Robert A., Khreisheh, Amal, Kiss, Viktória, Kleijne, Jos, Knight, Mark, Kootker, Lisette M., Kovács, Péter F., Kozubová, Anita, Kulcsár, Gabriella, Kulcsár, Valéria, Le Pennec, Christophe, Legge, Michael, Leivers, Matt, Loe, Louise, López-Costas, Olalla, Lord, Tom, Los, Dženi, Lyall, James, Marín-Arroyo, Ana B., Mason, Philip, Matošević, Damir, Maxted, Andy, McIntyre, Lauren, McKinley, Jacqueline, McSweeney, Kathleen, Meijlink, Bernard, Mende, Balázs G., Menđušić, Marko, Metlička, Milan, Meyer, Sophie, Mihovilić, Kristina, Milasinovic, Lidija, Minnitt, Steve, Moore, Joanna, Morley, Geoff, Mullan, Graham, Musilová, Margaréta, Neil, Benjamin, Nicholls, Rebecca, Novak, Mario, Pala, Maria, Papworth, Martin, Paresys, Cécile, Patten, Ricky, Perkić, Domagoj, Pesti, Krisztina, Petit, Alba, Petriščáková, Katarína, Pichon, Coline, Pickard, Catriona, Pilling, Zoltán, Price, T. Douglas, Radović, Siniša, Redfern, Rebecca, Resutík, Branislav, Rhodes, Daniel T., Richards, Martin B., Roberts, Amy, Roefstra, Jean, Sankot, Pavel, Šefčáková, Alena, Sheridan, Alison, Skae, Sabine, Šmolíková, Miroslava, Somogyi, Krisztina, Somogyvári, Ágnes, Stephens, Mark, Szabó, Géza, Szécsényi-Nagy, Anna, Szeniczey, Tamás, Tabor, Jonathan, Tankó, Károly, Maria, Clenis Tavarez, Terry, Rachel, Teržan, Biba, Teschler-Nicola, Maria, Torres-Martínez, Jesús F., Trapp, Julien, Turle, Ross, Ujvári, Ferenc, van der Heiden, Menno, Veleminsky, Petr, Veselka, Barbara, Vytlačil, Zdeněk, Waddington, Clive, Ware, Paula, Wilkinson, Paul, Wilson, Linda, Wiseman, Rob, Young, Eilidh, Zaninović, Joško, Žitňan, Andrej, Lalueza-Fox, Carles, de Knijff, Peter, Barnes, Ian, Halkon, Peter, Thomas, Mark G., Kennett, Douglas J., Cunliffe, Barry, Lillie, Malcolm, Rohland, Nadin, Pinhasi, Ron, Armit, Ian, and Reich, David

Published
2022
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16. Nucleotide-level distance metrics to quantify alternative splicing implemented in TranD

Author

National Institute of General Medical Sciences (US), University of Florida, Nanni, Adalena V., Titus-McQuillan, James, Bankole, Kinfeosioluwa S., Pardo-Palacios, Francisco J., Signor, Sarah, Vlaho, Srna, Moskalenko, Olexander, Morse, Alison M., Rogers, Rebekah L., Conesa, Ana, McIntyre, Lauren M., National Institute of General Medical Sciences (US), University of Florida, Nanni, Adalena V., Titus-McQuillan, James, Bankole, Kinfeosioluwa S., Pardo-Palacios, Francisco J., Signor, Sarah, Vlaho, Srna, Moskalenko, Olexander, Morse, Alison M., Rogers, Rebekah L., Conesa, Ana, and McIntyre, Lauren M.

Abstract

Advances in affordable transcriptome sequencing combined with better exon and gene prediction has motivated many to compare transcription across the tree of life. We develop a mathematical framework to calculate complexity and compare transcript models. Structural features, i.e. intron retention (IR), donor/acceptor site variation, alternative exon cassettes, alternative 5′/3′ UTRs, are compared and the distance between transcript models is calculated with nucleotide level precision. All metrics are implemented in a PyPi package, TranD and output can be used to summarize splicing patterns for a transcriptome (1GTF) and between transcriptomes (2GTF). TranD output enables quantitative comparisons between: annotations augmented by empirical RNA-seq data and the original transcript models; transcript model prediction tools for longread RNA-seq (e.g. FLAIR versus Isoseq3); alternate annotations for a species (e.g. RefSeq vs Ensembl); and between closely related species. In C. elegans, Z. mays, D. melanogaster, D. simulans and H. sapiens, alternative exons were observed more frequently in combination with an alternative donor/acceptor than alone. Transcript models in RefSeq and Ensembl are linked and both have unique transcript models with empirical support. D. melanogaster and D. simulans, share many transcript models and long-read RNAseq data suggests that both species are under-annotated. We recommend combined references.

Published
2024

19. Demography, diet and state of health in Roman York

Author

McIntyre, Lauren J. and Hadley, Dawn

Subjects
930
Abstract

This study combines new and pre-existing osteological evidence with archaeological evidence in order to reconstruct the demographic composition, broad dietary patterns and health status of the population of Roman York. This research examines the composition of the military and civilian sectors of the population, dietary patterns inferred from the study of dental remains, and differences in health according to social and occupational status categories within the population. Results indicate that the population had significant male bias, underrepresentation of infants and sub-adults, and approximately equal male and female life expectancy. Diets are likely to have been rich in fat and protein, and low in both cariogenic foods and foods that provide vitamins. Compared to contemporary urban sites, York had significantly elevated prevalence of antemortem trauma and porotic hyperostosis. Comparatively high rates of dislocation, peri-mortem trauma, brucellosis, osteopenia, os acromiale and osteochondroma were also observed. These findings suggest that the demographic composition of the population is heavily influenced by the presence of the military. A combination of osteological, isotopic, archaeobotanical, zooarchaeological and literary evidence indicates that dietary staples in the town appear to have been spelt based products such as bread, and beef. Other dietary components are likely to have included dairy products such as sheep's milk and cheese, olive oil, dried figs and fish. It is also likely that the populace were consuming lesser quantities of sugary products (e.g. containing honey and syrup), and fresh fruit and vegetables than populations from contemporary towns. Some of the observed pathological conditions with elevated values at Eboracum may be the result of poor comparative data, osteological rarity of a condition, or a combination of complex causal factors. Elevated prevalence of traumatic injury in some skeletal elements of the cranium and several post-cranial skeletal elements was significantly associated with an unusual group of burials from sites located on Driffield Terrace.

Published
2014

21. Purification of transcripts and metabolites from Drosophila heads.

Author

Jensen, Kurt, Sanchez-Garcia, Jonatan, Williams, Caroline, Khare, Swati, Mathur, Krishanu, Graze, Rita M, Hahn, Daniel A, McIntyre, Lauren M, Rincon-Limas, Diego E, and Fernandez-Funez, Pedro

Subjects
Animals, Drosophila, Gene Expression Profiling, Models, Animal, Female, Male, Transcriptome, Genetics, Issue 73, Biochemistry, Molecular Biology, Neurobiology, Neuroscience, Bioengineering, Cellular Biology, Anatomy, Neurodegenerative Diseases, Biological Assay, fruit fly, head separation, purification, mRNA, RNA, cDNA, DNA, transcripts, metabolites, replicates, SCA3, neurodegeneration, NMR, gene expression, animal model, Models, Animal, Biochemistry and Cell Biology, Psychology, Cognitive Sciences
Abstract

For the last decade, we have tried to understand the molecular and cellular mechanisms of neuronal degeneration using Drosophila as a model organism. Although fruit flies provide obvious experimental advantages, research on neurodegenerative diseases has mostly relied on traditional techniques, including genetic interaction, histology, immunofluorescence, and protein biochemistry. These techniques are effective for mechanistic, hypothesis-driven studies, which lead to a detailed understanding of the role of single genes in well-defined biological problems. However, neurodegenerative diseases are highly complex and affect multiple cellular organelles and processes over time. The advent of new technologies and the omics age provides a unique opportunity to understand the global cellular perturbations underlying complex diseases. Flexible model organisms such as Drosophila are ideal for adapting these new technologies because of their strong annotation and high tractability. One challenge with these small animals, though, is the purification of enough informational molecules (DNA, mRNA, protein, metabolites) from highly relevant tissues such as fly brains. Other challenges consist of collecting large numbers of flies for experimental replicates (critical for statistical robustness) and developing consistent procedures for the purification of high-quality biological material. Here, we describe the procedures for collecting thousands of fly heads and the extraction of transcripts and metabolites to understand how global changes in gene expression and metabolism contribute to neurodegenerative diseases. These procedures are easily scalable and can be applied to the study of proteomic and epigenomic contributions to disease.

Published
2013

27. MEDPRAT-SEL: Medical Resource Set Selector Searching High-Dimensionality Space

Author

Leinweber, Lawrence, McIntyre, Lauren, Goodenow, Debra, and Myers, Jerry

Subjects
Aerospace Medicine, Computer Programming And Software
Abstract

NASA Human Research Program's (HRP) next generation risk model closes the loop on medical risk and resource evaluation, providing researchers with a tool to assess and choose capabilities scientifically. The Medical Extensible Dynamic Probabilistic Risk Assessment Tool (MEDPRAT) simulator (SIM) evaluates resources in terms of medical benefit, such as reduced crew quality time lost (QTL), vs. cost, in mass or volume. The MEDPRAT resource set selector (SEL) searches the space of resource benefits v. cost, closing a feedback loop around the simulator, thus selecting resource sets with best benefit for cost. We discuss the design and results of the resource set selector. NASA HRP's emphasis on scientific assessment of risk, PRA, has led to the Cross-cutting Computational Modeling Project (CCMP).

Published
2020

28. A Machine Learning Approach to Jet-Surface Interaction Noise Modeling

Author

Brown, Cliff, Dowdall, Johnny, Whiteaker, Brian, Mcintyre, Lauren, and Miller, Chris

Subjects
Aircraft Propulsion And Power, Computer Programming And Software
Abstract

This paper investigates using machine learning to rapidly develop empirical models suitable for system-level aircraft noise studies. In particular, machine learning is used to train a neural network to predict the noise spectra produced by a round jet near a surface over a range of surface lengths, surface standoff distances, jet Mach numbers, and observer angles. These spectra include two sources, jet-mixing noise and jet-surface interaction (JSI) noise, with different scale factors as well as surface shielding and reflection effects to create a multi- dimensional problem. A second model is then trained using data from three rectangular nozzles to include nozzle aspect ratio in the spectral prediction. The training and validation data are from an extensive jet-surface interaction noise database acquired at the NASA Glenn Research Center's Aero-Acoustic Propulsion Laboratory. Although the number of training and validation points is small compared a typical machine learning application, the results of this investigation show that this approach is viable if the underlying data are well behaved.

Published
2020

29. Variation in leaf transcriptome responses to elevated ozone corresponds with physiological sensitivity to ozone across maize inbred lines

Author

Nanni, Adalena V. [0000-0001-7316-0951], Morse, Alison M. [0000-0003-4286-6489], Newman, Jeremy R. B. [0000-0001-8486-2801], Wedow, Jessica M. [0000-0001-5410-9026], Leakey, Andrew D. B. [0000-0001-6251-024X], Conesa, Ana [0000-0001-9597-311X], Ainsworth, Elizabeth A. [0000-0002-3199-8999], McIntyre, Lauren M. [0000-0002-0077-3359], Nanni, Adalena V., Morse, Alison M., Newman, Jeremy R. B., Choquette, Nicole E., Wedow, Jessica M., Liu, Zihao, Leakey, Andrew D. B., Conesa, Ana, Ainsworth, Elizabeth A., McIntyre, Lauren M., Nanni, Adalena V. [0000-0001-7316-0951], Morse, Alison M. [0000-0003-4286-6489], Newman, Jeremy R. B. [0000-0001-8486-2801], Wedow, Jessica M. [0000-0001-5410-9026], Leakey, Andrew D. B. [0000-0001-6251-024X], Conesa, Ana [0000-0001-9597-311X], Ainsworth, Elizabeth A. [0000-0002-3199-8999], McIntyre, Lauren M. [0000-0002-0077-3359], Nanni, Adalena V., Morse, Alison M., Newman, Jeremy R. B., Choquette, Nicole E., Wedow, Jessica M., Liu, Zihao, Leakey, Andrew D. B., Conesa, Ana, Ainsworth, Elizabeth A., and McIntyre, Lauren M.

Abstract

All FASTA files used for BLAST analyses and all BLAST results for https://doi.org/10.1093/genetics/iyac080 are included. Descriptions of each file can be found in README_maize_genetics_2022_zenodo.csv and further information about the content of the files can be found on github.

Published
2022

30. Variation in leaf transcriptome responses to elevated ozone corresponds with physiological sensitivity to ozone across maize inbred lines

Author

National Science Foundation (US), National Institute of General Medical Sciences (US), National Cancer Institute (US), Department of Agriculture (US), Nanni, Adalena V. [0000-0001-7316-0951], Morse, Alison M. [0000-0003-4286-6489], Newman, Jeremy R. B. [0000-0001-8486-2801], Wedow, Jessica M. [0000-0001-5410-9026], Leakey, Andrew D. B. [0000-0001-6251-024X], Conesa, Ana [0000-0001-9597-311X], Ainsworth, Elizabeth A. [0000-0002-3199-8999], McIntyre, Lauren M. [0000-0002-0077-3359], Nanni, Adalena V., Morse, Alison M., Newman, Jeremy R. B., Choquette, Nicole E., Wedow, Jessica M., Liu, Zihao, Leakey, Andrew D. B., Conesa, Ana, Ainsworth, Elizabeth A., McIntyre, Lauren M., National Science Foundation (US), National Institute of General Medical Sciences (US), National Cancer Institute (US), Department of Agriculture (US), Nanni, Adalena V. [0000-0001-7316-0951], Morse, Alison M. [0000-0003-4286-6489], Newman, Jeremy R. B. [0000-0001-8486-2801], Wedow, Jessica M. [0000-0001-5410-9026], Leakey, Andrew D. B. [0000-0001-6251-024X], Conesa, Ana [0000-0001-9597-311X], Ainsworth, Elizabeth A. [0000-0002-3199-8999], McIntyre, Lauren M. [0000-0002-0077-3359], Nanni, Adalena V., Morse, Alison M., Newman, Jeremy R. B., Choquette, Nicole E., Wedow, Jessica M., Liu, Zihao, Leakey, Andrew D. B., Conesa, Ana, Ainsworth, Elizabeth A., and McIntyre, Lauren M.

Abstract

We examine the impact of sustained elevated ozone concentration on the leaf transcriptome of 5 diverse maize inbred genotypes, which vary in physiological sensitivity to ozone (B73, Mo17, Hp301, C123, and NC338), using long reads to assemble transcripts and short reads to quantify expression of these transcripts. More than 99% of the long reads, 99% of the assembled transcripts, and 97% of the short reads map to both B73 and Mo17 reference genomes. Approximately 95% of the genes with assembled transcripts belong to known B73–Mo17 syntenic loci and 94% of genes with assembled transcripts are present in all temperate lines in the nested association mapping pan-genome. While there is limited evidence for alternative splicing in response to ozone stress, there is a difference in the magnitude of differential expression among the 5 genotypes. The transcriptional response to sustained ozone stress in the ozone resistant B73 genotype (151 genes) was modest, while more than 3,300 genes were significantly differentially expressed in the more sensitive NC338 genotype. There is the potential for tandem duplication in 30% of genes with assembled transcripts, but there is no obvious association between potential tandem duplication and differential expression. Genes with a common response across the 5 genotypes (83 genes) were associated with photosynthesis, in particular photosystem I. The functional annotation of genes not differentially expressed in B73 but responsive in the other 4 genotypes (789) identifies reactive oxygen species. This suggests that B73 has a different response to long-term ozone exposure than the other 4 genotypes. The relative magnitude of the genotypic response to ozone, and the enrichment analyses are consistent regardless of whether aligning short reads to: long read assembled transcripts; the B73 reference; the Mo17 reference. We find that prolonged ozone exposure directly impacts the photosynthetic machinery of the leaf.

Published
2022

34. Assessing needs for interdisciplinarity in agriculture, nutrition, and health education

Author

Roshania, Reshma P.; Yates, Joe; McIntyre, Lauren; Chancellor, Tim; Fivian, Emily; Hill, Michael; Isoto, Rosemary; Marinda, Pamela; Narayanan, Sudha; Whatford, Louise; Zotor, Francis; Khandelwal, Shweta, https://orcid.org/0000-0003-1048-2341 Narayanan, Sudha, Roshania, Reshma P.; Yates, Joe; McIntyre, Lauren; Chancellor, Tim; Fivian, Emily; Hill, Michael; Isoto, Rosemary; Marinda, Pamela; Narayanan, Sudha; Whatford, Louise; Zotor, Francis; Khandelwal, Shweta, and https://orcid.org/0000-0003-1048-2341 Narayanan, Sudha

Abstract

PR, IFPRI3; ISI; DCA; 2 Promoting Healthy Diets and Nutrition for all; 3 Building Inclusive and Efficient Markets, Trade Systems, and Food Industry; 4 Transforming Agricultural and Rural Economies, Development Strategies and Governance (DSG); Transformation Strategies

Published
2023

40. An anchored experimental design and meta-analysis approach to address batch effects in large-scale metabolomics

Author

Shaver, Amanda O., primary, Garcia, Brianna M., additional, Gouveia, Goncalo J., additional, Morse, Alison M., additional, Liu, Zihao, additional, Asef, Carter K., additional, Borges, Ricardo M., additional, Leach, Franklin E., additional, Andersen, Erik C., additional, Amster, I. Jonathan, additional, Fernández, Facundo M., additional, Edison, Arthur S., additional, and McIntyre, Lauren M., additional

Published
2022
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44. Presence of arachidonoyl-carnitine is associated with adverse cardiometabolic responses in hypertensive patients treated with atenolol

Author

Weng, Liming, Gong, Yan, Culver, Jeffrey, Gardell, Stephen J., Petucci, Christopher, Morse, Alison M., Frye, Reginald F., Turner, Stephen T., Chapman, Arlene, Boerwinkle, Eric, Gums, John, Beitelshees, Amber L., Borum, Peggy R., Johnson, Julie A., Garrett, Timothy J., McIntyre, Lauren M., and Cooper-DeHoff, Rhonda M.

Published
2016
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45. Agriculture and Population: Occupation and Burials in the Extramural Area of Margidunumon the Fosse Way in Nottinghamshire

Author

Simmonds, Andrew, Allen, Martyn, McIntyre, Lauren, and Champness, Carl

Abstract

AbstractThis paper presents the results of an excavation that uncovered c.390 m of roadside plots within the ribbon development alongside the Fosse Way on the south-west periphery of the walled small town of Margidunumin Nottinghamshire. The roadside plots appear to have been used for a combination of domestic occupation and agricultural activity, and to the rear lay 54 inhumation burials in 52 graves (including two double burials) and a single urned cremation burial, whose skeletons bore evidence for the tough working lives of the individuals. These are interpreted as the remains of peasant farmers and as evidence for the agricultural focus of the settlement, and of ‘small towns’ more generally. A contrast is drawn between the apparent poverty of this community and the apparently more high-status occupation within the defended core of the town.

Published
2023
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46. Ion Mobility for Unknown Metabolite Identification: Hope or Hype?

Author

Asef, Carter K., primary, Rainey, Markace, additional, Garcia, Brianna M., additional, Gouveia, Goncalo J., additional, Shaver, Amanda O., additional, Leach, Franklin E., additional, Morse, Allison M., additional, Edison, Arthur S., additional, McIntyre, Lauren M., additional, and Fernández, Facundo M., additional

Published
2022
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50. PaintOmics 4: new tools for the integrative analysis of multi-omics datasets supported by multiple pathway databases

Author

Ministerio de Ciencia, Innovación y Universidades (España), Ministerio de Ciencia e Innovación (España), Ministerio de Economía y Competitividad (España), Agencia Estatal de Investigación (España), National Institutes of Health (US), Slovenian Research Agency, Generalitat Valenciana, European Commission, Liu, Tianyuan, Salguero, Pedro, Petek, Marko, Martinez-Mira, Carlos, Balzano-Nogueira, Leandro, Ramšak, Živa, McIntyre, Lauren M., Gruden, Kristina, Tarazona, Sonia, Conesa, Ana, Ministerio de Ciencia, Innovación y Universidades (España), Ministerio de Ciencia e Innovación (España), Ministerio de Economía y Competitividad (España), Agencia Estatal de Investigación (España), National Institutes of Health (US), Slovenian Research Agency, Generalitat Valenciana, European Commission, Liu, Tianyuan, Salguero, Pedro, Petek, Marko, Martinez-Mira, Carlos, Balzano-Nogueira, Leandro, Ramšak, Živa, McIntyre, Lauren M., Gruden, Kristina, Tarazona, Sonia, and Conesa, Ana

Abstract

PaintOmics is a web server for the integrative analysis and visualisation of multi-omics datasets using biological pathway maps. PaintOmics 4 has several notable updates that improve and extend analyses. Three pathway databases are now supported: KEGG, Reactome and MapMan, providing more comprehensive pathway knowledge for animals and plants. New metabolite analysis methods fill gaps in traditional pathway-based enrichment methods. The metabolite hub analysis selects compounds with a high number of significant genes in their neighbouring network, suggesting regulation by gene expression changes. The metabolite class activity analysis tests the hypothesis that a metabolic class has a higher-than-expected proportion of significant elements, indicating that these compounds are regulated in the experiment. Finally, PaintOmics 4 includes a regulatory omics module to analyse the contribution of trans-regulatory layers (microRNA and transcription factors, RNA-binding proteins) to regulate pathways. We show the performance of PaintOmics 4 on both mouse and plant data to highlight how these new analysis features provide novel insights into regulatory biology. PaintOmics 4 is available at https://paintomics.org/.

Published
2022

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