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924 results on '"Mueller, Lukas"'

51. Equivariant Higher Hochschild Homology and Topological Field Theories

Author

Müller, Lukas and Woike, Lukas

Subjects
Mathematics - Algebraic Topology, Mathematical Physics, Mathematics - Quantum Algebra
Abstract

We present a version of higher Hochschild homology for spaces equipped with principal bundles for a structure group $G$. As coefficients, we allow $E_\infty$-algebras with $G$-action. For this homology theory, we establish an equivariant version of excision and prove that it extends to an equivariant topological field theory with values in the $(\infty,1)$-category of cospans of $E_\infty$-algebras., Comment: 26 pages, 2 figures, minor changes, comparison to equivariant factorization homology added; accepted for publication in "Homology, Homotopy and Applications"

Published
2018

52. A quick guide for student-driven community genome annotation

Author

Hosmani, Prashant S., Shippy, Teresa, Miller, Sherry, Benoit, Joshua B., Munoz-Torres, Monica, Flores, Mirella, Mueller, Lukas A., Wiersma-Koch, Helen, D'elia, Tom, Brown, Susan J., and Saha, Surya

Subjects
Quantitative Biology - Genomics
Abstract

High quality gene models are necessary to expand the molecular and genetic tools available for a target organism, but these are available for only a handful of model organisms that have undergone extensive curation and experimental validation over the course of many years. The majority of gene models present in biological databases today have been identified in draft genome assemblies using automated annotation pipelines that are frequently based on orthologs from distantly related model organisms. Manual curation is time consuming and often requires substantial expertise, but is instrumental in improving gene model structure and identification. Manual annotation may seem to be a daunting and cost-prohibitive task for small research communities but involving undergraduates in community genome annotation consortiums can be mutually beneficial for both education and improved genomic resources. We outline a workflow for efficient manual annotation driven by a team of primarily undergraduate annotators. This model can be scaled to large teams and includes quality control processes through incremental evaluation. Moreover, it gives students an opportunity to increase their understanding of genome biology and to participate in scientific research in collaboration with peers and senior researchers at multiple institutions.

Published
2018
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53. Geometry and 2-Hilbert Space for Nonassociative Magnetic Translations

Author

Bunk, Severin, Müller, Lukas, and Szabo, Richard J.

Subjects
High Energy Physics - Theory, Mathematical Physics, Mathematics - Category Theory, Mathematics - Quantum Algebra, Quantum Physics
Abstract

We suggest a geometric approach to quantisation of the twisted Poisson structure underlying the dynamics of charged particles in fields of generic smooth distributions of magnetic charge, and dually of closed strings in locally non-geometric flux backgrounds, which naturally allows for representations of nonassociative magnetic translation operators. We show how one can use the 2-Hilbert space of sections of a bundle gerbe in a putative framework for canonical quantisation. We define a parallel transport on bundle gerbes on $\mathbb{R}^d$ and show that it naturally furnishes weak projective 2-representations of the translation group on this 2-Hilbert space. We obtain a notion of covariant derivative on a bundle gerbe and a novel perspective on the fake curvature condition., Comment: 34 pages, 1 figure; v2: exposition improved, references added; Final version to be published in Letters in Mathematical Physics

Published
2018
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54. Development on Citrus medica infected with ‘Candidatus Liberibacter asiaticus’ has sex-specific and -nonspecific impacts on adult Diaphorina citri and its endosymbionts

Author

Coates, Laurynne C, Mahoney, Jaclyn, Ramsey, John S, Warwick, EricaRose, Johnson, Richard, MacCoss, Michael J, Krasnoff, Stuart B, Howe, Kevin J, Moulton, Kathy, Saha, Surya, Mueller, Lukas A, Hall, David G, Shatters, Robert G, Heck, Michelle L, and Slupsky, Carolyn M

Subjects
Medical Biochemistry and Metabolomics, Biomedical and Clinical Sciences, Environmental Sciences, Aetiology, 2.2 Factors relating to the physical environment, Animals, Citrus, Female, Hemiptera, Insect Vectors, Male, Metabolome, Microbiota, Oxidative Stress, Plant Diseases, Proteome, Rhizobiaceae, Symbiosis, Transcriptome, General Science & Technology
Abstract

Huanglongbing (HLB) is a deadly, incurable citrus disease putatively caused by the unculturable bacterium, 'Candidatus Liberibacter asiaticus' (CLas), and transmitted by Diaphorina citri. Prior studies suggest D. citri transmits CLas in a circulative and propagative manner; however, the precise interactions necessary for CLas transmission remain unknown, and the impact of insect sex on D. citri-CLas interactions is poorly understood despite reports of sex-dependent susceptibilities to CLas. We analyzed the transcriptome, proteome, metabolome, and microbiome of male and female adult D. citri reared on healthy or CLas-infected Citrus medica to determine shared and sex-specific responses of D. citri and its endosymbionts to CLas exposure. More sex-specific than shared D. citri responses to CLas were observed, despite there being no difference between males and females in CLas density or relative abundance. CLas exposure altered the abundance of proteins involved in immunity and cellular and oxidative stress in a sex-dependent manner. CLas exposure impacted cuticular proteins and enzymes involved in chitin degradation, as well as energy metabolism and abundance of the endosymbiont 'Candidatus Profftella armatura' in both sexes similarly. Notably, diaphorin, a toxic Profftella-derived metabolite, was more abundant in both sexes with CLas exposure. The responses reported here resulted from a combination of CLas colonization of D. citri as well as the effect of CLas infection on C. medica. Elucidating these impacts on D. citri and their endosymbionts contributes to our understanding of the HLB pathosystem and identifies the responses potentially critical to limiting or promoting CLas acquisition and propagation in both sexes.

Published
2020

55. A quick guide for student-driven community genome annotation

Author

Hosmani, Prashant S, Shippy, Teresa, Miller, Sherry, Benoit, Joshua B, Munoz-Torres, Monica, Flores-Gonzalez, Mirella, Mueller, Lukas A, Wiersma-Koch, Helen, D’Elia, Tom, Brown, Susan J, and Saha, Surya

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, 1.5 Resources and infrastructure (underpinning), Underpinning research, Computational Biology, Databases, Genetic, Genomics, Guidelines as Topic, Humans, Models, Genetic, Molecular Sequence Annotation, Students, Mathematical Sciences, Information and Computing Sciences, Bioinformatics
Abstract

High quality gene models are necessary to expand the molecular and genetic tools available for a target organism, but these are available for only a handful of model organisms that have undergone extensive curation and experimental validation over the course of many years. The majority of gene models present in biological databases today have been identified in draft genome assemblies using automated annotation pipelines that are frequently based on orthologs from distantly related model organisms and usually have minor or major errors. Manual curation is time consuming and often requires substantial expertise, but is instrumental in improving gene model structure and identification. Manual annotation may seem to be a daunting and cost-prohibitive task for small research communities but involving undergraduates in community genome annotation consortiums can be mutually beneficial for both education and improved genomic resources. We outline a workflow for efficient manual annotation driven by a team of primarily undergraduate annotators. This model can be scaled to large teams and includes quality control processes through incremental evaluation. Moreover, it gives students an opportunity to increase their understanding of genome biology and to participate in scientific research in collaboration with peers and senior researchers at multiple institutions.

Published
2019

58. Parallel Transport of Higher Flat Gerbes as an Extended Homotopy Quantum Field Theory

Author

Müller, Lukas and Woike, Lukas

Subjects
Mathematics - Quantum Algebra, Mathematical Physics, Mathematics - Algebraic Topology
Abstract

We prove that the parallel transport of a flat $n-1$-gerbe on any given target space gives rise to an $n$-dimensional extended homotopy quantum field theory. In case the target space is the classifying space of a finite group, we provide explicit formulae for this homotopy quantum field theory in terms of transgression. Moreover, we use the geometric theory of orbifolds to give a dimension-independent version of twisted and equivariant Dijkgraaf-Witten models. Finally, we introduce twisted equivariant Dijkgraaf-Witten theories giving us in the 3-2-1-dimensional case a new class of equivariant modular tensor categories which can be understood as twisted versions of the equivariant modular categories constructed by Maier, Nikolaus and Schweigert., Comment: 26 pages, 4 figures; v2: minor changes, introduction expanded, accepted for publication in Journal of Homotopy and Related Structures

Published
2018

60. Radiomics-based prediction of HCC response to atezolizumab/bevacizumab.

Author

Rodriguez, Isaac, Vellala, Abhinay, Itzel, Timo, Vácha, Michael, Chang, De-Hua, Dill, Michael, Seidensticker, Max, Mayerle, Julia, Munker, Stefan, Schönberg, Stefan O., Mueller, Lukas, Galle, Peter Robert, Weinmann, Arndt, Tamandl, Dietmar, Pinter, Matthias, Scheiner, Bernhard, Teufel, Andreas, Froelich, Matthias, Ebert, Matthias Philip, and Venerito, Marino

Published
2025
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61. Extended quantum field theory, index theory and the parity anomaly

Author

Müller, Lukas and Szabo, Richard J.

Subjects
High Energy Physics - Theory, Condensed Matter - Strongly Correlated Electrons, Mathematical Physics, Mathematics - Category Theory, Mathematics - Differential Geometry
Abstract

We use techniques from functorial quantum field theory to provide a geometric description of the parity anomaly in fermionic systems coupled to background gauge and gravitational fields on odd-dimensional spacetimes. We give an explicit construction of a geometric cobordism bicategory which incorporates general background fields in a stack, and together with the theory of symmetric monoidal bicategories we use it to provide the concrete forms of invertible extended quantum field theories which capture anomalies in both the path integral and Hamiltonian frameworks. Specialising this situation by using the extension of the Atiyah-Patodi-Singer index theorem to manifolds with corners due to Loya and Melrose, we obtain a new Hamiltonian perspective on the parity anomaly. We compute explicitly the 2-cocycle of the projective representation of the gauge symmetry on the quantum state space, which is defined in a parity-symmetric way by suitably augmenting the standard chiral fermionic Fock spaces with Lagrangian subspaces of zero modes of the Dirac Hamiltonian that naturally appear in the index theorem. We describe the significance of our constructions for the bulk-boundary correspondence in a large class of time-reversal invariant gauge-gravity symmetry-protected topological phases of quantum matter with gapless charged boundary fermions, including the standard topological insulator in 3+1 dimensions., Comment: 63 pages, 3 figures; v2: clarifying comments and references added; Final version to be published in Communications in Mathematical Physics

Published
2017
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62. A GNS construction of three-dimensional abelian Dijkgraaf-Witten theories

Author

Müller, Lukas and Schweigert, Christoph

Subjects
Mathematics - Quantum Algebra, High Energy Physics - Theory, Mathematical Physics
Abstract

We give a detailed account of the so-called "universal construction" that aims to extend invariants of closed manifolds, possibly with additional structure, to topological field theories and show that it amounts to a generalization of the GNS construction. We apply this construction to an invariant defined in terms of the groupoid cardinality of groupoids of bundles to recover Dijkgraaf-Witten theories, including the vector spaces obtained as a linearization of spaces of principal bundles., Comment: 17 pages, 4 figures, v2: typos corrected

Published
2017
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64. Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community

Author

Saha, Surya, Hosmani, Prashant S, Villalobos-Ayala, Krystal, Miller, Sherry, Shippy, Teresa, Flores, Mirella, Rosendale, Andrew, Cordola, Chris, Bell, Tracey, Mann, Hannah, DeAvila, Gabe, DeAvila, Daniel, Moore, Zachary, Buller, Kyle, Ciolkevich, Kathryn, Nandyal, Samantha, Mahoney, Robert, Van Voorhis, Joshua, Dunlevy, Megan, Farrow, David, Hunter, David, Morgan, Taylar, Shore, Kayla, Guzman, Victoria, Izsak, Allison, Dixon, Danielle E, Cridge, Andrew, Cano, Liliana, Cao, Xiaolong, Jiang, Haobo, Leng, Nan, Johnson, Shannon, Cantarel, Brandi L, Richards, Stephen, English, Adam, Shatters, Robert G, Childers, Chris, Chen, Mei-Ju, Hunter, Wayne, Cilia, Michelle, Mueller, Lukas A, Munoz-Torres, Monica, Nelson, David, Poelchau, Monica F, Benoit, Joshua B, Wiersma-Koch, Helen, D'Elia, Tom, and Brown, Susan J

Subjects
Biological Sciences, Genetics, Infectious Diseases, Human Genome, Vector-Borne Diseases, Biotechnology, Data Format, Library and Information Studies, Bioinformatics and computational biology, Data management and data science
Abstract

Author affiliation for Liliana Cano has been corrected to link to University of Florida/IFAS Indian River Research and Education Center, Ft. Pierce, FL 34945.

Published
2019

65. Fern genomes elucidate land plant evolution and cyanobacterial symbioses.

Author

Li, Fay-Wei, Brouwer, Paul, Carretero-Paulet, Lorenzo, Cheng, Shifeng, de Vries, Jan, Delaux, Pierre-Marc, Eily, Ariana, Koppers, Nils, Kuo, Li-Yaung, Li, Zheng, Simenc, Mathew, Small, Ian, Wafula, Eric, Angarita, Stephany, Barker, Michael S, Bräutigam, Andrea, dePamphilis, Claude, Gould, Sven, Hosmani, Prashant S, Huang, Yao-Moan, Huettel, Bruno, Kato, Yoichiro, Liu, Xin, Maere, Steven, McDowell, Rose, Mueller, Lukas A, Nierop, Klaas GJ, Rensing, Stefan A, Robison, Tanner, Rothfels, Carl J, Sigel, Erin M, Song, Yue, Timilsena, Prakash R, Van de Peer, Yves, Wang, Hongli, Wilhelmsson, Per KI, Wolf, Paul G, Xu, Xun, Der, Joshua P, Schluepmann, Henriette, Wong, Gane K-S, and Pryer, Kathleen M

Subjects
Cyanobacteria, Ferns, Phylogeny, Symbiosis, Gene Duplication, Genes, Plant, Genome, Plant, Biological Evolution, Genes, Plant, Genome
Abstract

Ferns are the closest sister group to all seed plants, yet little is known about their genomes other than that they are generally colossal. Here, we report on the genomes of Azolla filiculoides and Salvinia cucullata (Salviniales) and present evidence for episodic whole-genome duplication in ferns-one at the base of 'core leptosporangiates' and one specific to Azolla. One fern-specific gene that we identified, recently shown to confer high insect resistance, seems to have been derived from bacteria through horizontal gene transfer. Azolla coexists in a unique symbiosis with N2-fixing cyanobacteria, and we demonstrate a clear pattern of cospeciation between the two partners. Furthermore, the Azolla genome lacks genes that are common to arbuscular mycorrhizal and root nodule symbioses, and we identify several putative transporter genes specific to Azolla-cyanobacterial symbiosis. These genomic resources will help in exploring the biotechnological potential of Azolla and address fundamental questions in the evolution of plant life.

Published
2018

69. Continuous beam steering with a varactor-based reconfigurable intelligent surface in the Ka-band at 31 GHz.

Author

Wolff, Alexander, Franke, Lars, Klingel, Steffen, Krieger, Janis, Mueller, Lukas, Stemler, Ralf, and Rahm, Marco

Subjects
BEAM steering, UNIT cell, RADIATION, VARACTORS
Abstract

Varactor diodes have been proposed as active tuning elements of reconfigurable metasurfaces in the Ka-band. However, their experimental realization in this frequency range has not been demonstrated yet. We report the implementation of such a reconfigurable intelligent surface (RIS) made of 20 × 20 unit cells. By active tuning of the bias voltage of the varactors, the phase of the backward diffracted wave can be continuously tuned between 0 ° and 180 °. Thus, the phase tuning can be independently controlled for each unit cell. The frequency working range of the RIS is 1.1 GHz (from 30.6 to 31.7 GHz). As an illustration of the practical use, we demonstrate continuous beam steering of microwave radiation at 31 GHz in a defined propagation plane. [ABSTRACT FROM AUTHOR]

Published
2023
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72. Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community

Author

Saha, Surya, Hosmani, Prashant S, Villalobos-Ayala, Krystal, Miller, Sherry, Shippy, Teresa, Flores, Mirella, Rosendale, Andrew, Cordola, Chris, Bell, Tracey, Mann, Hannah, DeAvila, Gabe, DeAvila, Daniel, Moore, Zachary, Buller, Kyle, Ciolkevich, Kathryn, Nandyal, Samantha, Mahoney, Robert, Van Voorhis, Joshua, Dunlevy, Megan, Farrow, David, Hunter, David, Morgan, Taylar, Shore, Kayla, Guzman, Victoria, Izsak, Allison, Dixon, Danielle E, Cridge, Andrew, Cano, Liliana, Cao, Xiaolong, Jiang, Haobo, Leng, Nan, Johnson, Shannon, Cantarel, Brandi L, Richards, Stephen, English, Adam, Shatters, Robert G, Childers, Chris, Chen, Mei-Ju, Hunter, Wayne, Cilia, Michelle, Mueller, Lukas A, Munoz-Torres, Monica, Nelson, David, Poelchau, Monica F, Benoit, Joshua B, Wiersma-Koch, Helen, D’Elia, Tom, and Brown, Susan J

Subjects
Biological Sciences, Genetics, 2.6 Resources and infrastructure (aetiology), Good Health and Well Being, Animals, Citrus, Databases, Genetic, Genome, Insect, Hemiptera, Insect Vectors, Pest Control, Plant Diseases, Rhizobiaceae, Data Format, Library and Information Studies, Bioinformatics and computational biology, Data management and data science
Abstract

Database urlhttps://citrusgreening.org/.

Published
2017

73. Spatio-temporal modeling of high-throughput multispectral aerial images improves agronomic trait genomic prediction in hybrid maize

Author

Morales, Nicolas, primary, Anche, Mahlet T, additional, Kaczmar, Nicholas S, additional, Lepak, Nicholas, additional, Ni, Pengzun, additional, Romay, Maria Cinta, additional, Santantonio, Nicholas, additional, Buckler, Edward S, additional, Gore, Michael A, additional, Mueller, Lukas A, additional, and Robbins, Kelly R, additional

Published
2024
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77. Connecting data for consumer preferences, food quality, and breeding in support of market-oriented breeding of root, tuber, and banana crops

Author

Arnaud, Elizabeth, Menda, Naama, Tran, Thierry, Asiimwe, Amos, Kanaabi, Michael, Meghar, Karima, Forsythe, Lora, Kawuki, Robert Sezi, Ellebrock, Bryan, Kayondo, Ismail Siraj, Agbona, Afolabi, Zhang, Xiaofei, Mendes, Thiago, Laporte, Marie-Angélique, Nakitto, Mariam, Ssali, Reuben Tendo, Asfaw, Asrat, Uwimana, Brigitte, Ogbete, Chukwudi, Makunde, Godwill, Maraval, Isabelle, Mueller, Lukas, Bouniol, Alexandre, Fauvelle, Eglantine, Dufour, Dominique, Arnaud, Elizabeth, Menda, Naama, Tran, Thierry, Asiimwe, Amos, Kanaabi, Michael, Meghar, Karima, Forsythe, Lora, Kawuki, Robert Sezi, Ellebrock, Bryan, Kayondo, Ismail Siraj, Agbona, Afolabi, Zhang, Xiaofei, Mendes, Thiago, Laporte, Marie-Angélique, Nakitto, Mariam, Ssali, Reuben Tendo, Asfaw, Asrat, Uwimana, Brigitte, Ogbete, Chukwudi, Makunde, Godwill, Maraval, Isabelle, Mueller, Lukas, Bouniol, Alexandre, Fauvelle, Eglantine, and Dufour, Dominique

Abstract

The 5-year project 'Breeding roots, tubers and banana products for end user preferences' (RTBfoods) focused on collecting consumers' preferences on 12 food products to guide breeding programmes. It involved multidisciplinary teams from Africa, Latin America, and Europe. Diverse data types were generated on preferred qualities of users (farmers, family and entrepreneurial processors, traders or retailers, and consumers). Country-based target product profiles were produced with a comprehensive market analysis, disaggregating gender's role and preferences, providing prioritised lists of traits for the development of new plant varieties. We describe the approach taken to create, in the roots, tubers, and banana breeding databases, a centralised and meaningful open access to sensory information on food products and genotypes. Biochemical, instrumental textural, and sensory analysis data are then directly connected to the specific plant record while user survey data, bearing personal information, were analysed, anonymised, and uploaded in a repository. Names and descriptions of food quality traits were added into the Crop Ontology for labelling data in the databases, along with the various methods of measurement used by the project. The development and application of standard operating procedures, data templates, and adapted trait ontologies improved the data quality and its format, enabling the linking of these to the plant material studied when uploaded in the breeding databases or in repositories. Some modifications to the database model were necessary to accommodate the food sensory traits and sensory panel trials.

Published
2024

80. The absence of the caffeine synthase gene is involved in the naturally decaffeinated status of Coffea humblotiana, a wild species from Comoro archipelago

Author

Raharimalala, Nathalie, Rombauts, Stephane, McCarthy, Andrew, Garavito, Andréa, Orozco-Arias, Simon, Bellanger, Laurence, Morales-Correa, Alexa Yadira, Froger, Solène, Michaux, Stéphane, Berry, Victoria, Metairon, Sylviane, Fournier, Coralie, Lepelley, Maud, Mueller, Lukas, Couturon, Emmanuel, Hamon, Perla, Rakotomalala, Jean-Jacques, Descombes, Patrick, Guyot, Romain, and Crouzillat, Dominique

Published
2021
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84. Genome sequencing and analysis of the model grass Brachypodium distachyon

Author

Vogel, John P, Garvin, David F, Mockler, Todd C, Schmutz, Jeremy, Rokhsar, Dan, Bevan, Michael W, Barry, Kerrie, Lucas, Susan, Harmon-Smith, Miranda, Lail, Kathleen, Tice, Hope, Schmutz (Leader), Jeremy, Grimwood, Jane, McKenzie, Neil, Huo, Naxin, Gu, Yong Q, Lazo, Gerard R, Anderson, Olin D, Vogel (Leader), John P, You, Frank M, Luo, Ming-Cheng, Dvorak, Jan, Wright, Jonathan, Febrer, Melanie, Idziak, Dominika, Hasterok, Robert, Lindquist, Erika, Wang, Mei, Fox, Samuel E, Priest, Henry D, Filichkin, Sergei A, Givan, Scott A, Bryant, Douglas W, Chang, Jeff H, Mockler (Leader), Todd C, Wu, Haiyan, Wu, Wei, Hsia, An-Ping, Schnable, Patrick S, Kalyanaraman, Anantharaman, Barbazuk, Brad, Michael, Todd P, Hazen, Samuel P, Bragg, Jennifer N, Laudencia-Chingcuanco, Debbie, Weng, Yiqun, Haberer, Georg, Spannagl, Manuel, Mayer (Leader), Klaus, Rattei, Thomas, Mitros, Therese, Lee, Sang-Jik, Rose, Jocelyn K. C, Mueller, Lukas A, York, Thomas L, Wicker (Leader), Thomas, Buchmann, Jan P, Tanskanen, Jaakko, Schulman (Leader), Alan H, Gundlach, Heidrun, Bevan, Michael, Costa de Oliveira, Antonio, da C. Maia, Luciano, Belknap, William, Jiang, Ning, Lai, Jinsheng, Zhu, Liucun, Ma, Jianxin, Sun, Cheng, Pritham, Ellen, Salse (Leader), Jerome, Murat, Florent, Abrouk, Michael, Mayer, Klaus, Bruggmann, Remy, Messing, Joachim, Fahlgren, Noah, Sullivan, Christopher M, Carrington, James C, Chapman, Elisabeth J, May, Greg D, Zhai, Jixian, and Ganssmann, Matthias

Published
2010

85. Genome sequence analysis of the model grass Brachypodium distachyon: insights into grass genome evolution

Author

Schulman, Alan H., Yilmaz, Alper, Kalyanaraman, Anantharaman, Hsia, An-Ping, Oliveira, Antonio Costa de, Schnittger, Arp, Meyers, Blake C., Chalhoub, Boulos, Barbazuk, Brad, Sun, Cheng, Dardick, Christopher D., Sullivan, Christopher M., Cass, Cynthia L., Rokhsar, Dan, Garvin, David F., Laudencia-Chingcuanco, Debbie, O'Connor, Devin, Inzé, Dirk, Idziak, Dominika, Bryant, Douglas W., Chapman, Elisabeth J., Pritham, Ellen, Grotewold, Erich, Lindquist, Erika, Murat, Florent, Harmon, Frank, You, Frank M., Haberer, Georg, Tuskan, Gerald A., Lazo, Gerard R., May, Greg D., Mouille, Gregory, Wu, Haiyan, Belcram, Harry, Gundlach, Heidrun, Scheller, Henrik V., Priest, Henry D., Höfte, Herman, Budak, Hikmet, Tice, Hope, Baxter, Ivan, Tanskanen, Jaakko, Carrington, James C., Schnable, James, Thomson, James, Dvorak, Jan, Buchmann, Jan P., Grimwood, Jane, Higgins, Janet, Chang, Jeff H., Kimbrel, Jeffrey A., Bragg, Jennifer N., Schmutz, Jeremy, Pelloux, Jérome, Salse, Jerome, Harholt, Jesper, Wu, Jiajie, Ma, Jianxin, Lai, Jinsheng, Zhai, Jixian, Messing, Joachim, Rose, Jocelyn K. C., Sedbrook, John C., Vogel, John P., Wright, Jonathan, Lail, Kathleen, Barry, Kerrie, Hematy, Kian, Jung, Ki-Hong, Mayer, Klaus, Bartley, Laura E., Zhu, Liucun, Maia, Luciano da C., Tyler, Ludmila, Mueller, Lukas A., Sharma, Manoj K, Spannagl, Manuel, German, Marcelo, Heese, Maren, Byrne, Mary E., Charles, Mathieu, Ganssmann, Matthias, Wang, Mei, Febrer, Melanie, Abrouk, Michael, Bevan, Michael, Vega-Sanchez, Miguel, Luo, Ming-Cheng, Harmon-Smith, Miranda, Huo, Naxin, McKenzie, Neil, Jiang, Ning, Fahlgren, Noah, Anderson, Olin D., Green, Pamela J., Ronald, Pamela, Schnable, Patrick S., Cao, Peijian, and Ulvskov, Peter

Subjects
Brachypodium distachyon, Ehrhartoideae, Pancioideae, Pooideae, renewable energy
Abstract

Three subfamilies of grasses, the Erhardtoideae (rice), the Panicoideae (maize, sorghum, sugar cane and millet), and the Pooideae (wheat, barley and cool season forage grasses) provide the basis of human nutrition and are poised to become major sources of renewable energy. Here we describe the complete genome sequence of the wild grass Brachypodium distachyon (Brachypodium), the first member of the Pooideae subfamily to be completely sequenced. Comparison of the Brachypodium, rice and sorghum genomes reveals a precise sequence- based history of genome evolution across a broad diversity of the grass family and identifies nested insertions of whole chromosomes into centromeric regions as a predominant mechanism driving chromosome evolution in the grasses. The relatively compact genome of Brachypodium is maintained by a balance of retroelement replication and loss. The complete genome sequence of Brachypodium, coupled to its exceptional promise as a model system for grass research, will support the development of new energy and food crops

Published
2009

89. The genome and population genomics of allopolyploidCoffea arabicareveal the diversification history of modern coffee cultivars

Author

Salojärvi, Jarkko, primary, Rambani, Aditi, additional, Yu, Zhe, additional, Guyot, Romain, additional, Strickler, Susan, additional, Lepelley, Maud, additional, Wang, Cui, additional, Rajaraman, Sitaram, additional, Rastas, Pasi, additional, Zheng, Chunfang, additional, Muñoz, Daniella Santos, additional, Meidanis, João, additional, Paschoal, Alexandre Rossi, additional, Bawin, Yves, additional, Krabbenhoft, Trevor, additional, Wang, Zhen Qin, additional, Fleck, Steven, additional, Aussel, Rudy, additional, Bellanger, Laurence, additional, Charpagne, Aline, additional, Fournier, Coralie, additional, Kassam, Mohamed, additional, Lefebvre, Gregory, additional, Métairon, Sylviane, additional, Moine, Déborah, additional, Rigoreau, Michel, additional, Stolte, Jens, additional, Hamon, Perla, additional, Couturon, Emmanuel, additional, Tranchant-Dubreuil, Christine, additional, Mukherjee, Minakshi, additional, Lan, Tianying, additional, Engelhardt, Jan, additional, Stadler, Peter, additional, De Lemos, Samara Mireza Correia, additional, Suzuki, Suzana Ivamoto, additional, Sumirat, Ucu, additional, Man, Wai Ching, additional, Dauchot, Nicolas, additional, Orozco-Arias, Simon, additional, Garavito, Andrea, additional, Kiwuka, Catherine, additional, Musoli, Pascal, additional, Nalukenge, Anne, additional, Guichoux, Erwan, additional, Reinout, Havinga, additional, Smit, Martin, additional, Carretero-Paulet, Lorenzo, additional, Filho, Oliveiro Guerreiro, additional, Braghini, Masako Toma, additional, Padilha, Lilian, additional, Sera, Gustavo Hiroshi, additional, Ruttink, Tom, additional, Henry, Robert, additional, Marraccini, Pierre, additional, Van de Peer, Yves, additional, Andrade, Alan, additional, Domingues, Douglas, additional, Giuliano, Giovanni, additional, Mueller, Lukas, additional, Pereira, Luiz Filipe, additional, Plaisance, Stephane, additional, Poncet, Valerie, additional, Rombauts, Stephane, additional, Sankoff, David, additional, Albert, Victor A., additional, Crouzillat, Dominique, additional, de Kochko, Alexandre, additional, and Descombes, Patrick, additional

Published
2023
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96. Tomato Databases

Author

Mueller, Lukas, Fernandez-Pozo, Noe, Kole, Chittaranjan, Series editor, Causse, Mathilde, editor, Giovannoni, Jim, editor, Bouzayen, Mondher, editor, and Zouine, Mohamed, editor

Published
2016
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99. The genome and population genomics of allopolyploid Coffea arabicareveal the diversification history of modern coffee cultivars

Author

Salojärvi, Jarkko, Rambani, Aditi, Yu, Zhe, Guyot, Romain, Strickler, Susan, Lepelley, Maud, Wang, Cui, Rajaraman, Sitaram, Rastas, Pasi, Zheng, Chunfang, Muñoz, Daniella Santos, Meidanis, João, Paschoal, Alexandre Rossi, Bawin, Yves, Krabbenhoft, Trevor J., Wang, Zhen Qin, Fleck, Steven J., Aussel, Rudy, Bellanger, Laurence, Charpagne, Aline, Fournier, Coralie, Kassam, Mohamed, Lefebvre, Gregory, Métairon, Sylviane, Moine, Déborah, Rigoreau, Michel, Stolte, Jens, Hamon, Perla, Couturon, Emmanuel, Tranchant-Dubreuil, Christine, Mukherjee, Minakshi, Lan, Tianying, Engelhardt, Jan, Stadler, Peter, Correia De Lemos, Samara Mireza, Suzuki, Suzana Ivamoto, Sumirat, Ucu, Wai, Ching Man, Dauchot, Nicolas, Orozco-Arias, Simon, Garavito, Andrea, Kiwuka, Catherine, Musoli, Pascal, Nalukenge, Anne, Guichoux, Erwan, Reinout, Havinga, Smit, Martin, Carretero-Paulet, Lorenzo, Filho, Oliveiro Guerreiro, Braghini, Masako Toma, Padilha, Lilian, Sera, Gustavo Hiroshi, Ruttink, Tom, Henry, Robert, Marraccini, Pierre, Van de Peer, Yves, Andrade, Alan, Domingues, Douglas, Giuliano, Giovanni, Mueller, Lukas, Pereira, Luiz Filipe, Plaisance, Stephane, Poncet, Valerie, Rombauts, Stephane, Sankoff, David, Albert, Victor A., Crouzillat, Dominique, de Kochko, Alexandre, and Descombes, Patrick

Abstract

Coffea arabica, an allotetraploid hybrid of Coffea eugenioidesand Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabicaaccession and modern representatives of its diploid progenitors, C. eugenioidesand C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000–610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred ~30.5 thousand years ago, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica.

Published
2024
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100. Low bone mineral density is a prognostic factor for elderly patients with HCC undergoing TACE: results from a multicenter study

Author

Mueller, Lukas, Maehringer-Kunz, Aline, Auer, Timo Alexander, Fehrenbach, Uli, Gebauer, Bernhard, Haubold, Johannes, Theysohn, Jens M., Kim, Moon-Sung, Kleesiek, Jens, Diallo, Thierno D., Eisenblaetter, Michel, Bettinger, Dominik, Steinle, Verena, Mayer, Philipp, Zopfs, David, dos Santos, Daniel Pinto, Kloeckner, Roman, Mueller, Lukas, Maehringer-Kunz, Aline, Auer, Timo Alexander, Fehrenbach, Uli, Gebauer, Bernhard, Haubold, Johannes, Theysohn, Jens M., Kim, Moon-Sung, Kleesiek, Jens, Diallo, Thierno D., Eisenblaetter, Michel, Bettinger, Dominik, Steinle, Verena, Mayer, Philipp, Zopfs, David, dos Santos, Daniel Pinto, and Kloeckner, Roman

Abstract

Objectives Low bone mineral density (BMD) was recently identified as a novel risk factor for patients with hepatocellular carcinoma (HCC). In this multicenter study, we aimed to validate the role of BMD as a prognostic factor for patients with HCC undergoing transarterial chemoembolization (TACE). Methods This retrospective multicenter trial included 908 treatment-naive patients with HCC who were undergoing TACE as a first-line treatment, at six tertiary care centers, between 2010 and 2020. BMD was assessed by measuring the mean Hounsfield units (HUs) in the midvertebral core of the 11(th) thoracic vertebra, on contrast-enhanced computer tomography performed before treatment. We assessed the influence of BMD on median overall survival (OS) and performed multivariate analysis including established estimates for survival. Results The median BMD was 145 HU (IQR, 115-175 HU). Patients with a high BMD (>= 114 HU) had a median OS of 22.2 months, while patients with a low BMD (< 114 HU) had a lower median OS of only 16.2 months (p < .001). Besides albumin, bilirubin, tumor number, and tumor diameter, BMD remained an independent prognostic factor in multivariate analysis. Conclusions BMD is an independent predictive factor for survival in elderly patients with HCC undergoing TACE. The integration of BMD into novel scoring systems could potentially improve survival prediction and clinical decision-making.

Published
2023

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