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1. JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom

Author

Sreedasyam, Avinash, Plott, Christopher, Hossain, Shakhawat, Lovell, John T, Grimwood, Jane, Jenkins, Jerry W, Daum, Christopher, Barry, Kerrie, Carlson, Joseph, Shu, Shengqiang, Phillips, Jeremy, Amirebrahimi, Mojgan, Zane, Matthew, Wang, Mei, Goodstein, David, Haas, Fabian B, Hiss, Manuel, Perroud, Pierre-François, Jawdy, Sara S, Yang, Yongil, Hu, Rongbin, Johnson, Jenifer, Kropat, Janette, Gallaher, Sean D, Lipzen, Anna, Shakirov, Eugene V, Weng, Xiaoyu, Torres-Jerez, Ivone, Weers, Brock, Conde, Daniel, Pappas, Marilia R, Liu, Lifeng, Muchlinski, Andrew, Jiang, Hui, Shyu, Christine, Huang, Pu, Sebastian, Jose, Laiben, Carol, Medlin, Alyssa, Carey, Sankalpi, Carrell, Alyssa A, Chen, Jin-Gui, Perales, Mariano, Swaminathan, Kankshita, Allona, Isabel, Grattapaglia, Dario, Cooper, Elizabeth A, Tholl, Dorothea, Vogel, John P, Weston, David J, Yang, Xiaohan, Brutnell, Thomas P, Kellogg, Elizabeth A, Baxter, Ivan, Udvardi, Michael, Tang, Yuhong, Mockler, Todd C, Juenger, Thomas E, Mullet, John, Rensing, Stefan A, Tuskan, Gerald A, Merchant, Sabeeha S, Stacey, Gary, and Schmutz, Jeremy

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Generic health relevance, Gene Expression Regulation, Plant, Genes, Plant, Genome, Plant, Phylogeny, Software, Transcriptome, Atlases as Topic, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

Gene functional descriptions offer a crucial line of evidence for candidate genes underlying trait variation. Conversely, plant responses to environmental cues represent important resources to decipher gene function and subsequently provide molecular targets for plant improvement through gene editing. However, biological roles of large proportions of genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, an updateable data resource consisting of transcript abundance assays spanning 18 diverse species. To integrate across these diverse genotypes, we analyzed expression profiles, built gene clusters that exhibited tissue/condition specific expression, and tested for transcriptional response to environmental queues. We discovered extensive phylogenetically constrained and condition-specific expression profiles for genes without any previously documented functional annotation. Such conserved expression patterns and tightly co-expressed gene clusters let us assign expression derived additional biological information to 64 495 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome.jgi.doe.gov/), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.

Published
2023

4. What is Your Information Worth? A Systematic Analysis of the Endowment Effect of Different Data Types

Author

Schmitt, Vera, Conde, Daniel Sivizaca, Sahitaj, Premtim, Möller, Sebastian, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Fritsch, Lothar, editor, Hassan, Ismail, editor, and Paintsil, Ebenezer, editor

Published
2024
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7. BASEMENT v3: a modular freeware for river process modelling over multiple computational backends

Author

Vanzo, Davide, Peter, Samuel, Vonwiller, Lukas, Buergler, Matthias, Weberndorfer, Manuel, Siviglia, Annunziato, Conde, Daniel, and Vetsch, David F.

Subjects
Physics - Fluid Dynamics, Physics - Computational Physics
Abstract

Modelling river physical processes is of critical importance for flood protection, river management and restoration of riverine environments. Developments in algorithms and computational power have led to a wider spread of river simulation tools. However, the use of two-dimensional models can still be hindered by complexity in the setup and the high computational costs. Here we present the freeware BASEMENT version 3, a flexible tool for two-dimensional river simulations that bundles solvers for hydrodynamic, morphodynamic and scalar advection-diffusion processes. BASEMENT leverages different computational platforms (multi-core CPUs and graphics processing units GPUs) to enable the simulation of large domains and long-term river processes. The adoption of a fully costless worflow and a light GUI facilitate its broad utilization. We test its robustness and efficiency in a selection of benchmarks. Results confirm that BASEMENT could be an efficient and versatile tool for research, engineering practice and education in river modelling.

Published
2021
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9. Engaging stakeholders across a socio-environmentally diverse network of water research sites in North and South America

Author

Smyth, Robyn L, Fatima, Uroosa, Segarra, Monique, Borre, Lisa, Zilio, Mariana I, Reid, Brian, Pincetl, Stephanie, Astorga, Anna, Cisneros, M Andrea Huamantinco, Conde, Daniel, Harmon, Thomas, Hoyos, Natalia, Escobar, Jaime, Lozoya, Juan Pablo, Perillo, Gerardo ME, Piccolo, M Cintia, Rusak, James A, and Velez, Maria I

Subjects
Stakeholder engagement, Science outreach, Participatory research, Socio-hydrology, Environmental Science and Management, Urban and Regional Planning, Policy and Administration
Abstract

Maintaining and restoring freshwater ecosystem services in the face of local and global change requires adaptive research that effectively engages stakeholders. However, there is a lack of understanding and consensus in the research community regarding where, when, and which stakeholders should be engaged and what kind of researcher should do the engaging (e.g., physical, ecological, or social scientists). This paper explores stakeholder engagement across a developing network of aquatic research sites in North and South America with wide ranging cultural norms, social values, resource management paradigms, and eco-physical conditions. With seven sites in six countries, we found different degrees of engagement were explained by differences in the interests of the stakeholders given the history and perceived urgency of water resource problems as well as differences in the capacities of the site teams to effectively engage given their expertise and resources. We categorized engagement activities and applied Hurlbert and Gupta's split ladder of participation to better understand site differences and distill lessons learned for planning comparative socio-hydrological research and systematic evaluations of the effectiveness of stakeholder engagement approaches. We recommend research networks practice deliberate engagement of stakeholders that adaptively accounts for variations and changes in local socio-hydrologic conditions. This, in turn, requires further efforts to foster the development of well-integrated research teams that attract and retain researchers from multiple social science disciplines and enable training on effective engagement strategies for diverse conditions.

Published
2021

10. Shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants

Author

University of Florida, Kates, Heather [0000-0001-8490-2201], O'Meara, Brian C. [0000-0002-0337-5997], Stull, Gregory W. [0000-0002-2733-4823], James, Euan K. [0000-0001-7969-6570], Liu, Shui-Yin [0000-0002-8674-7097], Tian, Qin [0000-0002-7939-5329], Yi, Ting-Shuang [0000-0001-7093-9564], Conde, Daniel [0000-0001-8362-4190], Kirst, Matias [0000-0002-8186-3945], Ané, Jean-Michel [0000-0002-3128-9439], Soltis, Douglas [0000-0001-8638-4137], Guralnick, Robert [0000-0001-6682-1504], Soltis, Pamela [0000-0001-9310-8659], Folk, Ryan [0000-0002-5333-9273], Kates, Heather, O'Meara, Brian C., LaFrance, Raphael, Stull, Gregory W., James, Euan K., Liu, Shui-Yin, Tian, Qin, Yi, Ting-Shuang, Conde, Daniel, Kirst, Matias, Ané, Jean-Michel, Soltis, Douglas, Guralnick, Robert, Soltis, Pamela, Folk, Ryan, University of Florida, Kates, Heather [0000-0001-8490-2201], O'Meara, Brian C. [0000-0002-0337-5997], Stull, Gregory W. [0000-0002-2733-4823], James, Euan K. [0000-0001-7969-6570], Liu, Shui-Yin [0000-0002-8674-7097], Tian, Qin [0000-0002-7939-5329], Yi, Ting-Shuang [0000-0001-7093-9564], Conde, Daniel [0000-0001-8362-4190], Kirst, Matias [0000-0002-8186-3945], Ané, Jean-Michel [0000-0002-3128-9439], Soltis, Douglas [0000-0001-8638-4137], Guralnick, Robert [0000-0001-6682-1504], Soltis, Pamela [0000-0001-9310-8659], Folk, Ryan [0000-0002-5333-9273], Kates, Heather, O'Meara, Brian C., LaFrance, Raphael, Stull, Gregory W., James, Euan K., Liu, Shui-Yin, Tian, Qin, Yi, Ting-Shuang, Conde, Daniel, Kirst, Matias, Ané, Jean-Michel, Soltis, Douglas, Guralnick, Robert, Soltis, Pamela, and Folk, Ryan

Abstract

Root nodule symbiosis (RNS) is a complex trait that enables plants to access atmospheric nitrogen converted into usable forms through a mutualistic relationship with soil bacteria. Pinpointing the evolutionary origins of RNS is critical for understanding its genetic basis, but building this evolutionary context is complicated by data limitations and the intermittent presence of RNS in a single clade of ca. 30,000 species of flowering plants, i.e., the nitrogen-fixing clade (NFC). We developed the most extensive de novo phylogeny for the NFC and an RNS trait database to reconstruct the evolution of RNS. Our analysis identifies evolutionary rate heterogeneity associated with a two-step process: An ancestral precursor state transitioned to a more labile state from which RNS was rapidly gained at multiple points in the NFC. We illustrate how a two-step process could explain multiple independent gains and losses of RNS, contrary to recent hypotheses suggesting one gain and numerous losses, and suggest a broader phylogenetic and genetic scope may be required for genome-phenome mapping.

Published
2024

11. The single-cell transcriptome program of nodule development cellular lineages in Medicago truncatula

Author

Department of Energy (US), Biological and Environmental Research (US), Clemson University, Pereira, Wendell J. [0000-0003-1019-6281], Conde, Daniel [0000-0001-8362-4190], Triozzi, Paolo M. [0000-0003-0192-3336], Balmant, Kelly M. [0000-0001-5189-5121], Dervinis, Christopher [0000-0002-2176-4232], Schmidt, Henry W. [0000-0001-9465-9540], Boaventura-Novaes, Carolina [0000-0003-3674-4813], Chakraborty, Sanhita [0000-0001-7991-3977], Knaack, Sara A. [0000-0002-1178-2517], Gao, Yueyao [0000-0002-7607-2938], Feltus, Frank Alexander [0000-0002-2123-6114], Roy, Sushmita [0000-0001-7550-0542], Ané, Jean-Michel [0000-0002-3128-9439], Frugoli, Julia [0000-0003-1642-5911], Kirst, Matias [0000-0002-8186-3945], Pereira, Wendell J., Boyd, Jade, Conde, Daniel, Triozzi, Paolo M., Balmant, Kelly M., Dervinis, Christopher, Schmidt, Henry W., Boaventura-Novaes, Carolina, Chakraborty, Sanhita, Knaack, Sara A., Gao, Yueyao, Feltus, Frank Alexander, Roy, Sushmita, Ané, Jean-Michel, Frugoli, Julia, Kirst, Matias, Department of Energy (US), Biological and Environmental Research (US), Clemson University, Pereira, Wendell J. [0000-0003-1019-6281], Conde, Daniel [0000-0001-8362-4190], Triozzi, Paolo M. [0000-0003-0192-3336], Balmant, Kelly M. [0000-0001-5189-5121], Dervinis, Christopher [0000-0002-2176-4232], Schmidt, Henry W. [0000-0001-9465-9540], Boaventura-Novaes, Carolina [0000-0003-3674-4813], Chakraborty, Sanhita [0000-0001-7991-3977], Knaack, Sara A. [0000-0002-1178-2517], Gao, Yueyao [0000-0002-7607-2938], Feltus, Frank Alexander [0000-0002-2123-6114], Roy, Sushmita [0000-0001-7550-0542], Ané, Jean-Michel [0000-0002-3128-9439], Frugoli, Julia [0000-0003-1642-5911], Kirst, Matias [0000-0002-8186-3945], Pereira, Wendell J., Boyd, Jade, Conde, Daniel, Triozzi, Paolo M., Balmant, Kelly M., Dervinis, Christopher, Schmidt, Henry W., Boaventura-Novaes, Carolina, Chakraborty, Sanhita, Knaack, Sara A., Gao, Yueyao, Feltus, Frank Alexander, Roy, Sushmita, Ané, Jean-Michel, Frugoli, Julia, and Kirst, Matias

Abstract

Legumes establish a symbiotic relationship with nitrogen-fixing rhizobia by developing nodules. Nodules are modified lateral roots that undergo changes in their cellular development in response to bacteria, but the transcriptional reprogramming that occurs in these root cells remains largely uncharacterized. Here, we describe the cell-type-specific transcriptome response of Medicago truncatula roots to rhizobia during early nodule development in the wild-type genotype Jemalong A17, complemented with a hypernodulating mutant (sunn-4) to expand the cell population responding to infection and subsequent biological inferences. The analysis identifies epidermal root hair and stele sub-cell types associated with a symbiotic response to infection and regulation of nodule proliferation. Trajectory inference shows cortex-derived cell lineages differentiating to form the nodule primordia and, posteriorly, its meristem, while modulating the regulation of phytohormone-related genes. Gene regulatory analysis of the cell transcriptomes identifies new regulators of nodulation, including STYLISH 4, for which the function is validated.

Published
2024

16. Socioeconomic and Environmental Proxies for Comparing Freshwater Ecosystem Service Threats across International Sites: A Diagnostic Approach

Author

Harmon, Thomas C, Smyth, Robyn L, Chandra, Sudeep, Conde, Daniel, Dhungel, Ramesh, Escobar, Jaime, Hoyos, Natalia, Lozoya, Juan Pablo, Nin, Mariana, Perillo, Gerardo ME, Pincetl, Stephanie, Piccolo, M Cintia, Reid, Brian, Rusak, James A, Scordo, Facundo, Velez, Maria I, Villamizar, Sandra R, Wemple, Beverley, and Zilio, Mariana

Subjects
Life on Land, socio-environmental systems, ecosystem services, risk analysis, anthropogenic pressure, human pressure, experimental design
Abstract

In this work, we develop and test proxy-based diagnostic tools for comparing freshwater ecosystem services (FWES) risks across an international array of freshwater ecosystems. FWES threats are increasing rapidly under pressure from population, climate change, pollution, land use change, and other factors. We identified spatially explicit FWES threats estimates (referred to as threat benchmarks) and extracted watershed-specific values for an array of aquatic ecosystems in the Western Hemisphere (Ramsar sites). We compared these benchmark values to values extracted for sites associated with an international FWES threat investigation. The resulting benchmark threats appeared to provide a meaningful context for the diagnostic assessment of study site selection by revealing gaps in coverage of the underlying socio-environmental problem. In an effort to simplify the method, we tested regularly updated environmental and socioeconomic metrics as potential proxies for the benchmark threats using regression analysis. Three category proxies, aggregated from (i) external (global to regional, climate-related), (ii) internal (watershed management-related), and (iii) socioeconomic and governance related proxies produced strong relationships with water supply threat benchmarks, but only weak relationships with biodiversity-related and nutrient regulation benchmark threats. Our results demonstrate the utility of advancing global FWES status and threat benchmarks for organizing coordinated research efforts and prioritizing decisions with regard to international socio-environmental problems.

Published
2018

17. The uncharacterized gene EVE contributes to vessel element dimensions in Populus

Author

Ribeiro, Cíntia L., Conde, Daniel, Balmant, Kelly M., Dervinis, Christopher, Johnson, Matthew G., McGrath, Aaron P., Szewczyk, Paul, Unda, Faride, Finegan, Christina A., Schmidt, Henry W., Miles, Brianna, Drost, Derek R., Novaes, Evandro, Gonzalez-Benecke, Carlos A., Peter, Gary F., Burleigh, J. Gordon, Martin, Timothy A., Mansfield, Shawn D., Chang, Geoffrey, Wicketti, Norman J., and Kirst, Matias

Published
2020

20. DNA hypomethylation of the host tree impairs interaction with mutualistic ectomycorrhizal fungus

Author

Conseil Régional du Centre-Val de Loire, Department of Energy (US), Kohler, Annegret [0000-0002-9575-9567], Sow, Mamadou Dia [0000-0002-2815-4939], Delaunay, Alain [0000-0002-2519-5380], Fauchery, Laure [0000-0002-2571-0274], Barry, Kerrie W. [0000-0002-8999-6785], Keymanesh, Keykhosrow [0000-0001-6019-9443], Singan, Vasanth [0000-0002-9983-5707], Grigoriev, Igor [0000-0002-3136-8903], Fichot, Régis [0000-0001-5527-4103], Conde, Daniel [0000-0001-8362-4190], Perales, Mariano [0000-0002-7351-8439], Tost, Jörg [0000-0002-2683-0817], Martin, Francis M. [0000-0002-4737-3715], Allona, Isabel [0000-0002-7012-2850], Strauss, Steven H. [0000-0001-9670-3082], Veneault-Fourrey, Claire [0000-0001-9778-2659], Maury, Stéphane 0000-0003-0481-0847], Vigneaud, Julien, Kohler, Annegret, Sow, Mamadou Dia, Delaunay, Alain, Fauchery, Laure, Guinet, Frederic, Daviaud, Christian, Barry, Kerrie W., Keymanesh, Keykhosrow, Johnson, Jenifer, Singan, Vasanth, Grigoriev, Igor, Fichot, Régis, Conde, Daniel, Perales, Mariano, Tost, Jörg, Martin, Francis M., Allona, Isabel, Strauss, Steven H., Veneault-Fourrey, Claire, Maury, Stéphane, Conseil Régional du Centre-Val de Loire, Department of Energy (US), Kohler, Annegret [0000-0002-9575-9567], Sow, Mamadou Dia [0000-0002-2815-4939], Delaunay, Alain [0000-0002-2519-5380], Fauchery, Laure [0000-0002-2571-0274], Barry, Kerrie W. [0000-0002-8999-6785], Keymanesh, Keykhosrow [0000-0001-6019-9443], Singan, Vasanth [0000-0002-9983-5707], Grigoriev, Igor [0000-0002-3136-8903], Fichot, Régis [0000-0001-5527-4103], Conde, Daniel [0000-0001-8362-4190], Perales, Mariano [0000-0002-7351-8439], Tost, Jörg [0000-0002-2683-0817], Martin, Francis M. [0000-0002-4737-3715], Allona, Isabel [0000-0002-7012-2850], Strauss, Steven H. [0000-0001-9670-3082], Veneault-Fourrey, Claire [0000-0001-9778-2659], Maury, Stéphane 0000-0003-0481-0847], Vigneaud, Julien, Kohler, Annegret, Sow, Mamadou Dia, Delaunay, Alain, Fauchery, Laure, Guinet, Frederic, Daviaud, Christian, Barry, Kerrie W., Keymanesh, Keykhosrow, Johnson, Jenifer, Singan, Vasanth, Grigoriev, Igor, Fichot, Régis, Conde, Daniel, Perales, Mariano, Tost, Jörg, Martin, Francis M., Allona, Isabel, Strauss, Steven H., Veneault-Fourrey, Claire, and Maury, Stéphane

Abstract

Ectomycorrhizas are an intrinsic component of tree nutrition and responses to environmental variations. How epigenetic mechanisms might regulate these mutualistic interactions is unknown. By manipulating the level of expression of the chromatin remodeler DECREASE IN DNA METHYLATION 1 (DDM1) and two demethylases DEMETER-LIKE (DML) in Populus tremula × Populus alba lines, we examined how host DNA methylation modulates multiple parameters of the responses to root colonization with the mutualistic fungus Laccaria bicolor. We compared the ectomycorrhizas formed between transgenic and wild-type (WT) trees and analyzed their methylomes and transcriptomes. The poplar lines displaying lower mycorrhiza formation rate corresponded to hypomethylated overexpressing DML or RNAi-ddm1 lines. We found 86 genes and 288 transposable elements (TEs) differentially methylated between WT and hypomethylated lines (common to both OX-dml and RNAi-ddm1) and 120 genes/1441 TEs in the fungal genome suggesting a host-induced remodeling of the fungal methylome. Hypomethylated poplar lines displayed 205 differentially expressed genes (cis and trans effects) in common with 17 being differentially methylated (cis). Our findings suggest a central role of host and fungal DNA methylation in the ability to form ectomycorrhizas including not only poplar genes involved in root initiation, ethylene and jasmonate-mediated pathways, and immune response but also terpenoid metabolism.

Published
2023

25. Single-nuclei transcriptome analysis of the shoot apex vascular system differentiation in Populus

Author

Federal Government of the United States, University of Florida, Conde, Daniel [0000-0001-8362-4190], Triozzi, Paolo M. [0000-0003-0192-3336], Pereira, Wendell J. [0000-0003-1019-6281], Schmidt, Henry W. [0000-0001-9465-9540], Balmant, Kelly M. [0000-0001-5189-5121], Knaack, Sara A.[0000-0002-1178-2517], Redondo-López, Arturo [0000-0003-2037-5400], Roy, Sushmita [0000-0002-3694-1705], Dervinis, Christopher [0000-0002-2176-4232], Kirst, Matias [0000-0002-8186-3945], Conde, Daniel, Triozzi, Paolo M., Pereira, Wendell J., Schmidt, Henry W., Balmant, Kelly M., Knaack, Sara A., Redondo-López, Arturo, Roy, Sushmita, Dervinis, Christopher, Kirst, Matias, Federal Government of the United States, University of Florida, Conde, Daniel [0000-0001-8362-4190], Triozzi, Paolo M. [0000-0003-0192-3336], Pereira, Wendell J. [0000-0003-1019-6281], Schmidt, Henry W. [0000-0001-9465-9540], Balmant, Kelly M. [0000-0001-5189-5121], Knaack, Sara A.[0000-0002-1178-2517], Redondo-López, Arturo [0000-0003-2037-5400], Roy, Sushmita [0000-0002-3694-1705], Dervinis, Christopher [0000-0002-2176-4232], Kirst, Matias [0000-0002-8186-3945], Conde, Daniel, Triozzi, Paolo M., Pereira, Wendell J., Schmidt, Henry W., Balmant, Kelly M., Knaack, Sara A., Redondo-López, Arturo, Roy, Sushmita, Dervinis, Christopher, and Kirst, Matias

Abstract

Differentiation of stem cells in the plant apex gives rise to aerial tissues and organs. Presently, we lack a lineage map of the shoot apex cells in woody perennials - a crucial gap considering their role in determining primary and secondary growth. Here, we used single-nuclei RNA-sequencing to determine cell type-specific transcriptomes of the Populus vegetative shoot apex. We identified highly heterogeneous cell populations clustered into seven broad groups represented by 18 transcriptionally distinct cell clusters. Next, we established the developmental trajectories of the epidermis, leaf mesophyll and vascular tissue. Motivated by the high similarities between Populus and Arabidopsis cell population in the vegetative apex, we applied a pipeline for interspecific single-cell gene expression data integration. We contrasted the developmental trajectories of primary phloem and xylem formation in both species, establishing the first comparison of vascular development between a model annual herbaceous and a woody perennial plant species. Our results offer a valuable resource for investigating the principles underlying cell division and differentiation conserved between herbaceous and perennial species while also allowing us to examine species-specific differences at single-cell resolution.

Published
2022

30. JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom

Author

Department of Energy (US), Center for Bioenergy Innovation (US), United Soybean Board, Samuel Roberts Noble Foundation, National Institutes of Health (US), Great Lakes Bioenergy Research Center (US), Sreedasyam, Avinash [0000-0001-7336-7012], Plott, Christopher [0000-0002-0109-5174], Lovell, John T. [0000-0002-8938-1166], Grimwood, Jane [0000-0002-8356-8325], Jenkins, Jerry [0000-0002-7943-3997], Barry, Kerrie W. [0000-0002-8999-6785], Carlson, Joseph [0000-0003-1423-9138], Shu, Shengqiang [0000-0002-4336-8994], Goodstein, David [0000-0001-6287-2697], Haas, Fabian B. [0000-0002-7711-5282], Hiss, Manuel [0000-0002-7876-783X], Perroud, Pierre François [0000-0001-7607-3618], Jawdy, Sara S. [0000-0002-8123-5439], Yang, Yongil [0000-0002-6925-5410], Hu, Rongbin [0000-0001-5921-6891], Kropat, Janette [0000-0001-8952-3286], Gallaher, Sean D. [0000-0002-9773-6051], Lipzen, Anna [0000-0003-2293-9329], Shakirov, Eugene V. [0000-0003-2689-7410], Weng, Xiaoyu [0000-0002-3831-7551], Torres-Jerez, Ivone [0000-0001-9264-4652], Weers, Brock [0009-0007-5865-7514], Pappas, Marilia R. [0000-0002-4680-0199], Muchlinski, Andrew [0000-0002-7139-6941], Jiang, Hui [0000-0003-4588-7074], López Sebastián, José Manuel [0000-0002-6203-8835], Carrell, Alyssa A. [0000-0003-1142-4709], Chen, Jin Gui [0000-0002-1752-4201], Perales, Mariano [0000-0002-7351-8439], Swaminathan, Kankshita [0000-0002-4936-509X], Allona, Isabel [0000-0002-7012-2850], Grattapaglia, Dario [0000-0002-0050-970X], Tholl, Dorothea [0000-0003-2636-6345], Vogel, John P. [0000-0003-1786-2689], Yang, Xiaohan [0000-0001-5207-4210], Brutnell, Thomas P. [0000-0002-3581-8211], Kellogg, Elizabeth A. [0000-0002-9664-3179], Baxter, Ivan [0000-0001-6680-1722], Udvardi, Michael [0000-0001-9850-0828], Tang, Yuhong [0000-0003-2967-778X], Mockler, Todd C. [0000-0002-0462-5775], Juenger, Thomas E. [0000-0001-9550-9288], Mullet, John [0000-0003-2502-2671], Rensing, Stefan A. [0000-0002-0225-873X], Tuskan, Gerald A. [0000-0003-0106-1289], Merchant, Sabeeha S. [0000-0002-2594-509X], Stacey, Gary [0000-0001-5914-2247], Schmutz, Jeremy [0000-0001-8062-9172], Sreedasyam, Avinash, Plott, Christopher, Hossain, Md Shakhawat, Lovell, John T., Grimwood, Jane, Jenkins, Jerry, Daum, Christopher, Barry, Kerrie W., Carlson, Joseph, Shu, Shengqiang, Phillips, Jeremy, Amirebrahimi, Mojgan, Zane, Matthew, Wang, Mei, Goodstein, David, Haas, Fabian B., Hiss, Manuel, Perroud, Pierre François, Jawdy, Sara S., Yang, Yongil, Hu, Rongbin, Johnson, Jenifer, Kropat, Janette, Gallaher, Sean D., Lipzen, Anna, Shakirov, Eugene V., Weng, Xiaoyu, Torres-Jerez, Ivone, Weers, Brock, Conde, Daniel, Pappas, Marilia R., Liu, Lifeng, Muchlinski, Andrew, Jiang, Hui, Shyu, Christine, Huang, Pu, López Sebastián, José Manuel, Laiben, Carol, Medlin, Alyssa, Carey, Sankalpi, Carrell, Alyssa A., Chen, Jin Gui, Perales, Mariano, Swaminathan, Kankshita, Allona, Isabel, Grattapaglia, Dario, Cooper, Elizabeth A., Tholl, Dorothea, Vogel, John P., Weston, David J., Yang, Xiaohan, Brutnell, Thomas P., Kellogg, Elizabeth A., Baxter, Ivan, Udvardi, Michael, Tang, Yuhong, Mockler, Todd C., Juenger, Thomas E., Mullet, John, Rensing, Stefan A., Tuskan, Gerald A., Merchant, Sabeeha S., Stacey, Gary, Schmutz, Jeremy, Department of Energy (US), Center for Bioenergy Innovation (US), United Soybean Board, Samuel Roberts Noble Foundation, National Institutes of Health (US), Great Lakes Bioenergy Research Center (US), Sreedasyam, Avinash [0000-0001-7336-7012], Plott, Christopher [0000-0002-0109-5174], Lovell, John T. [0000-0002-8938-1166], Grimwood, Jane [0000-0002-8356-8325], Jenkins, Jerry [0000-0002-7943-3997], Barry, Kerrie W. [0000-0002-8999-6785], Carlson, Joseph [0000-0003-1423-9138], Shu, Shengqiang [0000-0002-4336-8994], Goodstein, David [0000-0001-6287-2697], Haas, Fabian B. [0000-0002-7711-5282], Hiss, Manuel [0000-0002-7876-783X], Perroud, Pierre François [0000-0001-7607-3618], Jawdy, Sara S. [0000-0002-8123-5439], Yang, Yongil [0000-0002-6925-5410], Hu, Rongbin [0000-0001-5921-6891], Kropat, Janette [0000-0001-8952-3286], Gallaher, Sean D. [0000-0002-9773-6051], Lipzen, Anna [0000-0003-2293-9329], Shakirov, Eugene V. [0000-0003-2689-7410], Weng, Xiaoyu [0000-0002-3831-7551], Torres-Jerez, Ivone [0000-0001-9264-4652], Weers, Brock [0009-0007-5865-7514], Pappas, Marilia R. [0000-0002-4680-0199], Muchlinski, Andrew [0000-0002-7139-6941], Jiang, Hui [0000-0003-4588-7074], López Sebastián, José Manuel [0000-0002-6203-8835], Carrell, Alyssa A. [0000-0003-1142-4709], Chen, Jin Gui [0000-0002-1752-4201], Perales, Mariano [0000-0002-7351-8439], Swaminathan, Kankshita [0000-0002-4936-509X], Allona, Isabel [0000-0002-7012-2850], Grattapaglia, Dario [0000-0002-0050-970X], Tholl, Dorothea [0000-0003-2636-6345], Vogel, John P. [0000-0003-1786-2689], Yang, Xiaohan [0000-0001-5207-4210], Brutnell, Thomas P. [0000-0002-3581-8211], Kellogg, Elizabeth A. [0000-0002-9664-3179], Baxter, Ivan [0000-0001-6680-1722], Udvardi, Michael [0000-0001-9850-0828], Tang, Yuhong [0000-0003-2967-778X], Mockler, Todd C. [0000-0002-0462-5775], Juenger, Thomas E. [0000-0001-9550-9288], Mullet, John [0000-0003-2502-2671], Rensing, Stefan A. [0000-0002-0225-873X], Tuskan, Gerald A. [0000-0003-0106-1289], Merchant, Sabeeha S. [0000-0002-2594-509X], Stacey, Gary [0000-0001-5914-2247], Schmutz, Jeremy [0000-0001-8062-9172], Sreedasyam, Avinash, Plott, Christopher, Hossain, Md Shakhawat, Lovell, John T., Grimwood, Jane, Jenkins, Jerry, Daum, Christopher, Barry, Kerrie W., Carlson, Joseph, Shu, Shengqiang, Phillips, Jeremy, Amirebrahimi, Mojgan, Zane, Matthew, Wang, Mei, Goodstein, David, Haas, Fabian B., Hiss, Manuel, Perroud, Pierre François, Jawdy, Sara S., Yang, Yongil, Hu, Rongbin, Johnson, Jenifer, Kropat, Janette, Gallaher, Sean D., Lipzen, Anna, Shakirov, Eugene V., Weng, Xiaoyu, Torres-Jerez, Ivone, Weers, Brock, Conde, Daniel, Pappas, Marilia R., Liu, Lifeng, Muchlinski, Andrew, Jiang, Hui, Shyu, Christine, Huang, Pu, López Sebastián, José Manuel, Laiben, Carol, Medlin, Alyssa, Carey, Sankalpi, Carrell, Alyssa A., Chen, Jin Gui, Perales, Mariano, Swaminathan, Kankshita, Allona, Isabel, Grattapaglia, Dario, Cooper, Elizabeth A., Tholl, Dorothea, Vogel, John P., Weston, David J., Yang, Xiaohan, Brutnell, Thomas P., Kellogg, Elizabeth A., Baxter, Ivan, Udvardi, Michael, Tang, Yuhong, Mockler, Todd C., Juenger, Thomas E., Mullet, John, Rensing, Stefan A., Tuskan, Gerald A., Merchant, Sabeeha S., Stacey, Gary, and Schmutz, Jeremy

Abstract

Gene functional descriptions offer a crucial line of evidence for candidate genes underlying trait variation. Conversely, plant responses to environmental cues represent important resources to decipher gene function and subsequently provide molecular targets for plant improvement through gene editing. However, biological roles of large proportions of genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, an updateable data resource consisting of transcript abundance assays spanning 18 diverse species. To integrate across these diverse genotypes, we analyzed expression profiles, built gene clusters that exhibited tissue/condition specific expression, and tested for transcriptional response to environmental queues. We discovered extensive phylogenetically constrained and condition-specific expression profiles for genes without any previously documented functional annotation. Such conserved expression patterns and tightly co-expressed gene clusters let us assign expression derived additional biological information to 64 495 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome.jgi.doe.gov/), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.

Published
2023

31. Epigenetics in Forest Trees

Author

Sow, Mamadou Dia, primary, Allona, Isabel, additional, Ambroise, Christophe, additional, Conde, Daniel, additional, Fichot, Régis, additional, Gribkova, Svetlana, additional, Jorge, Véronique, additional, Le-Provost, Grégoire, additional, Pâques, Luc, additional, Plomion, Christophe, additional, Salse, Jérôme, additional, Sanchez-Rodriguez, Léopoldo, additional, Segura, Vincent, additional, Tost, Jörg, additional, and Maury, Stéphane, additional

Published
2018
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33. DNA hypomethylation of the host tree impairs interaction with mutualistic ectomycorrhizal fungus

Author

Vigneaud, Julien, primary, Kohler, Annegret, additional, Sow, Mamadou Dia, additional, Delaunay, Alain, additional, Fauchery, Laure, additional, Guinet, Frederic, additional, Daviaud, Christian, additional, Barry, Kerrie W., additional, Keymanesh, Keykhosrow, additional, Johnson, Jenifer, additional, Singan, Vasanth, additional, Grigoriev, Igor, additional, Fichot, Régis, additional, Conde, Daniel, additional, Perales, Mariano, additional, Tost, Jörg, additional, Martin, Francis M., additional, Allona, Isabel, additional, Strauss, Steven H., additional, Veneault‐Fourrey, Claire, additional, and Maury, Stéphane, additional

Published
2023
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35. Development of Phase XXXII, of the UDEISTA Business School, With the Agency for Reincorporation and Normalization, ARN GT Santander Magdalena Medio

Author

Candanoza-Conde, Daniel Javier, Murillo-Salcedo, Alexander Jose, Salazar-Páez, Cristhyan Alexander, Márquez-Pinilla, Humberto, and Albornoz-Silva, María Jenny

Subjects
Reintegration, Normalization, Conflict, Reincorporación, Entrepreneurship, Training, Conflicto, Formación, Emprendimiento, Normalización
Abstract

Digital, Este proyecto se fundamenta en el objetivo de llevar a cabo la Fase XXXII de la Escuela Empresarial UDEISTA, en asociación con la Universidad de Santander UDES y las Unidades Tecnológicas de Santander UTS, por medio del Seminario de “Herramientas en el uso del Marketing Innovador Aplicado al Emprendimiento”, con el fin de contribuir al mejoramiento de la calidad de vida de las personas adscritas al programa de la Agencia para la Reincorporación y Normalización ARN, a través de actividades ilustrativas mediante encuentros virtuales sincrónicos, creando instrumentos que les permitan adquirir capacidades para enfrentar las diferentes barreras sociales y económicas, estimular el uso de un plan de marketing para sus proyectos de emprendimiento, mejorando de esa manera su calidad de vida y conocer las nuevas tendencias del marketing innovador que son esenciales para las empresas en su día a día. Esta Fase XXXII de la Escuela Empresarial UDEISTA se fundamentó en métodos de precognición para facilitar la comprensión de los temas del Seminario por parte de los participantes. El tipo de estudio utilizado es descriptivo en el sentido de que identifica las características de la población participante pero no se orienta a cambiar su comportamiento. Al finalizar el Seminario se puede concluir que el desarrollo de la Fase XXXII de la Escuela Empresarial UDEISTA, es un proyecto de gran impacto social y académico, ya que contribuye al desarrollo de los acuerdos de paz después del conflicto, mediante procesos de educación y formación., This project is based on the objective of carrying out the XXXII Phase of the UDEISTA Business School, in association with the University of Santander UDES and the Technological Units of Santander UTS, through the Seminar on "Tools in the use of Applied Innovative Marketing to Entrepreneurship", in order to contribute to improving the quality of life of people attached to the program of the Agency for Reincorporation and Normalization ARN, through illustrative activities through synchronous virtual meetings, creating instruments that allow them to acquire skills to face the different social and economic barriers, stimulate the use of a marketing plan for their entrepreneurial projects, thus improving their quality of life and learn about the new innovative marketing trends that are essential for companies in their day to day . This Phase XXXII of the UDEISTA Business School was based on precognition methods to better understand the topics of the Seminar. The type of study used is descriptive in the sense that it identifies the characteristics of the participating population but is not aimed at changing their behavior. At the end of the workshop, it can be concluded that the development of Phase XXXII of the UDEISTA Business School is a project with great social and academic impact, since it contributes to the development of peace agreements after the conflict through education and training., Pregrado, Administrador(a) Financiero, Introducción 22 Aspectos Metodológicos del Estudio 24 Planteamiento del Problema 24 Formulación del Problema 25 Objetivos 25 Objetivo General 25 Objetivos Específicos 25 Justificación 26 Marco Referencial 27 Marco de Antecedentes 27 Marco Teórico 35 Marco Legal 38 Diseño Metodológico del Estudio 40 Tipo de Estudio 40 Instrumentos Para la Recolección de Información y Técnicas de Medición 41 Definición de Variables.. 41 Definición Conceptual.. 41 Instrumento Para la Recolección de Información. 41 Población y Muestra 41 Población.. 41 Resultados y Discusión 43 Definición de Temáticas del Seminario 43 Guías Didácticas de Pre Saberes 46 Guía No. 1 Herramientas Ofimáticas 46 Guía No. 2 Herramientas Ofimáticas (Microsoft Word, Excel y PowerPoint) 47 Guía No. 3 Emprendimiento 47 Guía No. 4 Empresario vs Emprendedor 47 Guía No. 5 Modelos de Negocios 48 Guía No. 6 Tipos y Modelos de Mercado 48 Guía No. 7 Oferta y Demanda 48 Guía No. 8 Marketing 49 Guía No. 9 Marketing Digital 49 Desarrollo de los Módulos y el Plan de Encuentro del Seminario 49 Desarrollo de la Primera Sesión Sincrónica 53 Módulo I “Herramientas Ofimáticas” 55 Introducción a las Herramientas Ofimáticas. 55 Profundización de las Herramientas Ofimáticas. 57 Módulo II “Emprendimiento” 58 Emprendedor. 58 Diferencias entre Empresario y Emprendedor. 60 Modelo de Negocio 62 Tipos de Modelo de Negocio. 63 Matriz DOFA. 65 Segmentación del Mercado. 66 Mercado. 67 Modulo III “Marketing” 69 Marketing. 69 Marketing y Publicidad. 70 Marketing Digital. 72 Geolocalización. 73 Material Visual Didáctico 75 Diseño de la Revista Digital 77 Medición del Nivel de Satisfacción de los Participantes del Seminario y Análisis de los Resultados de la Encuesta 78 Conclusiones 88 Recomendaciones 91 Referencias Bibliográficas 93 Apéndices 95, Tabla 1 Marco Legal 39 Tabla 2 Temáticas del Seminario 43 Tabla 3 Cronograma de Actividades 50, Figura 1 Primer Comité Académico Equipos ARN y UDES, Agosto 2022 45 Figura 2 Primer Comité Académico Equipo UDES 45 Figura 3 Grupo de WhatsApp 53 Figura 4 Correo Electrónico Formación 54 Figura 5 Lista de Asistencia 54 Figura 6 Lista de Notas 55 Figura 7 Desarrollo de la Sesión I 56 Figura 8 Desarrollo de la Sesión II 58 Figura 9 Desarrollo de la Sesión III 60 Figura 10 Desarrollo de la Sesión IV 61 Figura 11 Desarrollo de la Sesión V 63 Figura 12 Desarrollo de la Sesión VI 64 Figura 13 Desarrollo de la Sesión VII 66 Figura 14 Desarrollo de la Sesión VIII 67 Figura 15 Desarrollo de la Sesión IX 68 Figura 16 Desarrollo de la Sesión X 70 Figura 17 Desarrollo de la Sesión XI 71 Figura 18 Desarrollo de la Sesión XII 73 Figura 19 Desarrollo de la Sesión XIII 74 Figura 20 Desarrollo de la Actividad en Clase Educaplay 75 Figura 21 Plantilla Utilizada Para las Diapositivas 76 Figura 22 Video Motivacional al Inicio de la Clase 76 Figura 23 Imágenes Utilizadas en las Sesiones 77 Figura 24 Imagen de la Portada de la Revista Digital 78 Figura 25 ¿Considera Que le es Fácil Entender los Temas Explicados por los Docentes Instructores? 79 Figura 26 ¿Considera que las Temáticas Realizadas en el Seminario le han Aportado a su Vida Personal y Laboral? 79 Figura 27 ¿Qué tan Satisfecho Esta con el Material Didáctico Utilizado en la Realización del Seminario? 80 Figura 28 ¿Cómo Calificaría a los Docentes Instructores? 80 Figura 29 ¿Qué tal Fácil ha Sido Entender el Lenguaje o Términos que Usaron los Capacitadores? 81 Figura 30 ¿Considera que ha Aprendido Aspectos con un Auténtico Valor Para su Vida? 81 Figura 31 El Ambiente de Trabajo y Relaciones con los Docentes, Compañeros en las Sesiones Virtuales ha Sido 82 Figura 32 ¿Considera que las Actividades y Tareas han Sido Adecuadas a los Temas Tratados en las Clases? 82 Figura 33 ¿Los Docentes Estudiantes Utilizaron Material Visual Didáctico Adecuado en su Proceso de Aprendizaje? 83 Figura 34 ¿Los Docentes Tutores Asistían Puntalmente a las Sesiones Sincrónicas? 83 Figura 35 ¿Los Docentes Aclaran con Certeza las Dudas que Surgen en las Sesiones? 84 Figura 36 Califique la Metodología Utilizada por los Instructores en el Desarrollo de su Aprendizaje 84 Figura 37 ¿Considera que las Clases Impartidas de Manera Virtual Mediante la Aplicación de Zoom Permitió un Desarrollo Normal de la Clase? 85 Figura 38 En General ¿Que tan Satisfecho se Encuentra con el Seminario "Herramientas en el Uso del Marketing Innovador Aplicado al Emprendimiento”? 85 Figura 39 Si Tuviera la Oportunidad de Recomendar el Seminario, ¿lo Recomendaría? 86 Figura 40 ¿Los Instructores Respetaron los Diferentes Puntos de Vista y Opiniones de los Participantes? 86 Figura 41 ¿Considera que la Comunicación con los Docentes Fue? 87 Figura 42 Comentarios, Sugerencias y Aspectos a Mejorar del Seminario 87, Apéndice A. Encuesta 95

Published
2022

36. Food waste interventions in retail: a scoping review protocol

Author

Castro, Ana, Luquine, Cézar, Conde, Daniel, Zentgraf, Lea, and Metaferia, Ribka

Subjects
Food Studies, food waste, Environmental Studies, markets, supermarkets, retail, scoping review, Social and Behavioral Sciences, intervention
Abstract

What interventions by civil society, state and market to manage food waste in supermarkets and markets (retail) worldwide can be identified in the literature?

Published
2022
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38. Food waste interventions in retail: a scoping review

Author

Luquine, Cézar, de Castro, Ana, Conde, Daniel, Zentgraf, Lea, and Metaferia, Ribka

Subjects
food waste, markets, supermarkets, retail, scoping review, intervention
Abstract

What interventions by civil society, state and market to manage food waste in supermarkets and markets (retail) worldwide can be identified in the literature?

Published
2022
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42. JGI Plant Gene Atlas: An updateable transcriptome resource to improve structural annotations and functional gene descriptions across the plant kingdom

Author

Sreedasyam, Avinash, primary, Plott, Christopher, additional, Hossain, Md Shakhawat, additional, Lovell, John T., additional, Grimwood, Jane, additional, Jenkins, Jerry W., additional, Daum, Christopher, additional, Barry, Kerrie, additional, Carlson, Joseph, additional, Shu, Shengqiang, additional, Phillips, Jeremy, additional, Amirebrahimi, Mojgan, additional, Zane, Matthew, additional, Wang, Mei, additional, Goodstein, David, additional, Haas, Fabian B., additional, Hiss, Manuel, additional, Perroud, Pierre-François, additional, Jawdy, Sara S., additional, Hu, Rongbin, additional, Johnson, Jenifer, additional, Kropat, Janette, additional, Gallaher, Sean D., additional, Lipzen, Anna, additional, Tillman, Ryan, additional, Shakirov, Eugene V., additional, Weng, Xiaoyu, additional, Torres-Jerez, Ivone, additional, Weers, Brock, additional, Conde, Daniel, additional, Pappas, Marilia R., additional, Liu, Lifeng, additional, Muchlinski, Andrew, additional, Jiang, Hui, additional, Shyu, Christine, additional, Huang, Pu, additional, Sebastian, Jose, additional, Laiben, Carol, additional, Medlin, Alyssa, additional, Carey, Sankalpi, additional, Carrell, Alyssa A., additional, Perales, Mariano, additional, Swaminathan, Kankshita, additional, Allona, Isabel, additional, Grattapaglia, Dario, additional, Cooper, Elizabeth A., additional, Tholl, Dorothea, additional, Vogel, John P., additional, Weston, David J, additional, Yang, Xiaohan, additional, Brutnell, Thomas P., additional, Kellogg, Elizabeth A., additional, Baxter, Ivan, additional, Udvardi, Michael, additional, Tang, Yuhong, additional, Mockler, Todd C., additional, Juenger, Thomas E., additional, Mullet, John, additional, Rensing, Stefan A., additional, Tuskan, Gerald A., additional, Merchant, Sabeeha S., additional, Stacey, Gary, additional, and Schmutz, Jeremy, additional

Published
2022
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45. Two shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants

Author

Kates, Heather R., primary, O’Meara, Brian C., additional, LaFrance, Raphael, additional, Stull, Gregory W., additional, James, Euan K., additional, Conde, Daniel, additional, Liu, Shuiyin, additional, Tian, Qin, additional, Yi, Tingshuang, additional, Kirst, Matias, additional, Ané, Jean-Michel, additional, Soltis, Douglas E., additional, Guralnick, Robert P., additional, Soltis, Pamela S., additional, and Folk, Ryan A., additional

Published
2022
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48. Direitos Humanos e a cultura organizacional das instituições policiais

Author

Conde, Daniel Gonçalves

Subjects
Cultura Organizacional, Public security, Segurança pública, Direitos Humanos, Human rights, Organizational culture
Abstract

Human Rights has been related to the brazilian police institutions recently and since then, its infiltration in such institutions has become subject of study. It seeks to comprehend the concepts of organizational culture from the administration field by going through the peculiarities of public institutions. It establishes the origin of the national insertion of Human Rights in several brazilian police formations. At last, the police culture and the Human Rights is object of analysis, observing multiple bibliography that talk about this thematic, and by so, establishing the real influence and perception of Human Rights as organizacional culture in the brazilians policies. Os Direitos Humanos e as instituições policiais brasileiras possuem um inter-relacionamento recente e a sua infiltração nas instituições policiais tem sido cada vez mais objeto de estudo. Busca-se entender os conceitos de cultura organizacional oriundos do campo da Administração, passando pelas peculiaridades atinentes às instituições públicas. Se estabelece a origem da inserção nacional dos conceitos de Direitos Humanos nas formações policiais brasileiras. Por fim, é objeto de análise a cultura policial e os Direitos Humanos, observando-se diversas bibliografias que tratam da temática, assim, objetivando estabelecer a real influência e percepção dos conceitos de Direitos Humanos como cultura organizacional nas polícias brasileiras.

Published
2022

49. MD simulation files for: Molecular dynamics simulations of transmembrane cyclic peptide nanotubes using classical force fields, Hydrogen Mass Repartitioning and Hydrogen Isotope Exchange methods: a critical comparison

Author

Conde, Daniel, Garrido, Pablo F., Calvelo, Mart��n, Pi��eiro, ��ngel, and Garcia-Fandino, Rebeca

Subjects
Quantitative Biology::Biomolecules, Physics::Atomic Physics
Abstract

Initial structures, mdp files and topologies used in Molecular dynamics simulations of transmembrane cyclic peptide nanotubes using classical force fields, Hydrogen Mass Repartitioning and Hydrogen Isotope Exchange methods: a critical comparison.

Published
2022
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50. Decoding exceptional plant traits by comparative single-cell genomics

Author

Kirst, Matias [0000-0002-8186-3945], Conde, Daniel, Kirst, Matias, Kirst, Matias [0000-0002-8186-3945], Conde, Daniel, and Kirst, Matias

Abstract

Some plants have acquired traits of remarkable adaptive value to thrive under stress. Transferring these traits to crops could improve agriculture, but uncovering the toolkit required has remained largely elusive. We propose that single-cell genomics offers a framework to compare species with contrasting developmental traits and to identify the regulators of evolutionary innovations.

Published
2022

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