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1. Biochemical and Molecular Characterization of Musa sp. Cultured in Temporary Immersion Bioreactor

Author

Christopher A. Sambolín Pérez, Rosalinda Aybar Batista, Sullymar Morales Marrero, Dinorah Andino Santiago, Axel Reyes Colón, Juan A. Negrón Berríos, Ángel Núñez Marrero, and Alok Arun

Subjects
temporary immersion bioreactor, micropropagation, PEPC, Rubisco, Botany, QK1-989
Abstract

The genus Musa sp. contains commercially important fleshy fruit-producing plants, including plantains and bananas, with a strong potential for providing food security and sources of revenue to farmers. Concerns with the quality of vegetative tissues along with the possibility of the transmission of phytopathogens makes the availability of healthy plantlets limited for farmers. Micropropagation of plantains offers an alternative to producing large numbers of plantlets. However, conventional methods of micropropagation have high production costs and are labor-intensive. Recently, the temporary immersion bioreactor (TIB) has emerged as an alternative to conventional micropropagation (CM) methods. Our work utilized SEM microscopy (scanning electron microscope) and molecular and biochemical tools (qRT-PCR and ICP-OES) to characterize and compare the morphological properties, elemental composition, and photosynthetic gene expression of plantains cultured on TIB. Additionally, morphological features of growth and propagation rates were analyzed to compare outputs obtained from TIB and CM. Results showed higher growth and multiplication rates for plantlets cultivated in TIB. Gene expression analysis of selected photosynthetic genes demonstrated high transcript abundance of phosphoenolpyruvate carboxylase (PEPC) in plantain tissues obtained by TIB. Elemental composition analysis showed higher content of iron in plantains grown in TIB, suggesting a potential correlation with PEPC expression. These results demonstrate that micropropagation of Musa sp. via the liquid medium in TIB is an efficient and low-cost approach in comparison with solid media in CM.

Published
2023
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2. Micropropagation of Rare Scutellaria havanensis Jacq. and Preliminary Studies on Antioxidant Capacity and Anti-Cancer Potential

Author

Lani Irvin, Yarelia Zavala Ortiz, Kamila Rivera Rivera, Brajesh Nanda Vaidya, Samantha H Sherman, Rosalinda Aybar Batista, Juan A. Negrón Berríos, Nirmal Joshee, and Alok Arun

Subjects
conservation, HCT 116 cells, polyphenol, trichomes, Organic chemistry, QD241-441
Abstract

We report the development of in vitro propagation protocols through an adventitious shoot induction pathway for a rare and medicinal Scutellaria havanensis. In vitro propagation studies using nodal explants showed MS medium supplemented with 10 µM 6-Benzylaminopurine induced the highest number of adventitious shoots in a time-dependent manner. A ten-day incubation was optimum for shoot bud induction as longer exposures resulted in hyperhydricity of the explants and shoots induced. We also report preliminary evidence of Agrobacterium tumefaciens EHA105-mediated gene transfer transiently expressing the green fluorescent protein in this species. Transformation studies exhibited amenability of various explant tissues, internode being the most receptive. As the plant has medicinal value, research was carried out to evaluate its potential antioxidant capacity and the efficacy of methanolic leaf extracts in curbing the viability of human colorectal cancer cell line HCT116. Comparative total polyphenol and flavonoid content measurement of fresh and air-dried leaf extract revealed that the fresh leaf extracts contain higher total polyphenol and flavonoid content. The HCT 116 cell viability was assessed by colorimetric assay using a 3-(4,5-dimethyl-thiazol-2-yl)-2,5-diphenyltetrazolium bromide, showed a steady growth inhibition after 24 h of incubation. Scanning electron microscopy of leaf surface revealed a high density of glandular and non-glandular trichomes. This research provides a basis for the conservation of this rare plant and future phytochemical screening and clinical research.

Published
2021
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3. Transcriptome Analysis of Cambium Tissue of Paulownia Collected during Winter and Spring

Author

Zachary D. Perry, Thangasamy Saminathan, Alok Arun, Brajesh N. Vaidya, Chhandak Basu, Umesh K. Reddy, and Nirmal Joshee

Subjects
Paulownia, cambium, transcriptome, winter season, spring season, tree growth, Biology (General), QH301-705.5
Abstract

Paulownia (Paulownia elongata) is a fast-growing, multipurpose deciduous hardwood species that grows in a wide range of temperatures from –30 °C to 45 °C. Seasonal cues influence the secondary growth of tree stems, including cambial activity, wood chemistry, and transition to latewood formation. In this study, a de novo transcriptome approach was conducted to identify the transcripts expressed in vascular cambial tissue from senescent winter and actively growing spring seasons. An Illumina paired-end sequenced cambial transcriptome generated 297,049,842 clean reads, which finally yielded 61,639 annotated unigenes. Based on non-redundant protein database analyses, Paulownia cambial unigenes shared the highest homology (64.8%) with Erythranthe guttata. KEGG annotation of 35,471 unigenes identified pathways enriched in metabolic activities. Transcriptome-wide DEG analysis showed that 2688 and 7411 genes were upregulated and downregulated, respectively, in spring tissues compared to winter. Interestingly, several transcripts encoding heat shock proteins were upregulated in the spring season. RT-qPCR expression results of fifteen wood-forming candidate genes involved in hemicellulose, cellulose, lignin, auxin, and cytokinin pathways showed that the hemicellulose genes (CSLC4, FUT1, AXY4, GATL1, and IRX19) were significantly upregulated in spring season tissues when compared to winter tissues. In contrast, lignin pathway genes CCR1 and CAD1 were upregulated in winter cambium. Finally, a transcriptome-wide marker analysis identified 11,338 Simple Sequence Repeat (SSRs). The AG/CT dinucleotide repeat predominately represented all SSRs. Altogether, the cambial transcriptomic analysis reported here highlights the molecular events of wood formation during winter and spring. The identification of candidate genes involved in the cambial growth provides a roadmap of wood formation in Paulownia and other trees for the seasonal growth variation.

Published
2021
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4. Convergent recruitment of TALE homeodomain life cycle regulators to direct sporophyte development in land plants and brown algae

Author

Alok Arun, Susana M Coelho, Akira F Peters, Simon Bourdareau, Laurent Pérès, Delphine Scornet, Martina Strittmatter, Agnieszka P Lipinska, Haiqin Yao, Olivier Godfroy, Gabriel J Montecinos, Komlan Avia, Nicolas Macaisne, Christelle Troadec, Abdelhafid Bendahmane, and J Mark Cock

Subjects
life cycle, TALE homeodomain transcription factor, sporophyte development, Ectocarpus sp, brown algae, stramenopiles, Medicine, Science, Biology (General), QH301-705.5
Abstract

Three amino acid loop extension homeodomain transcription factors (TALE HD TFs) act as life cycle regulators in green algae and land plants. In mosses these regulators are required for the deployment of the sporophyte developmental program. We demonstrate that mutations in either of two TALE HD TF genes, OUROBOROS or SAMSARA, in the brown alga Ectocarpus result in conversion of the sporophyte generation into a gametophyte. The OUROBOROS and SAMSARA proteins heterodimerise in a similar manner to TALE HD TF life cycle regulators in the green lineage. These observations demonstrate that TALE-HD-TF-based life cycle regulation systems have an extremely ancient origin, and that these systems have been independently recruited to regulate sporophyte developmental programs in at least two different complex multicellular eukaryotic supergroups, Archaeplastida and Chromalveolata.

Published
2019
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5. Selection and validation of reference genes for qRT-PCR expression analysis of candidate genes involved in olfactory communication in the butterfly Bicyclus anynana.

Author

Alok Arun, Véronique Baumlé, Gaël Amelot, and Caroline M Nieberding

Subjects
Medicine, Science
Abstract

Real-time quantitative reverse transcription PCR (qRT-PCR) is a technique widely used to quantify the transcriptional expression level of candidate genes. qRT-PCR requires the selection of one or several suitable reference genes, whose expression profiles remain stable across conditions, to normalize the qRT-PCR expression profiles of candidate genes. Although several butterfly species (Lepidoptera) have become important models in molecular evolutionary ecology, so far no study aimed at identifying reference genes for accurate data normalization for any butterfly is available. The African bush brown butterfly Bicyclus anynana has drawn considerable attention owing to its suitability as a model for evolutionary ecology, and we here provide a maiden extensive study to identify suitable reference gene in this species. We monitored the expression profile of twelve reference genes: eEF-1α, FK506, UBQL40, RpS8, RpS18, HSP, GAPDH, VATPase, ACT3, TBP, eIF2 and G6PD. We tested the stability of their expression profiles in three different tissues (wings, brains, antennae), two developmental stages (pupal and adult) and two sexes (male and female), all of which were subjected to two food treatments (food stress and control feeding ad libitum). The expression stability and ranking of twelve reference genes was assessed using two algorithm-based methods, NormFinder and geNorm. Both methods identified RpS8 as the best suitable reference gene for expression data normalization. We also showed that the use of two reference genes is sufficient to effectively normalize the qRT-PCR data under varying tissues and experimental conditions that we used in B. anynana. Finally, we tested the effect of choosing reference genes with different stability on the normalization of the transcript abundance of a candidate gene involved in olfactory communication in B. anynana, the Fatty Acyl Reductase 2, and we confirmed that using an unstable reference gene can drastically alter the expression profile of the target candidate genes.

Published
2015
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6. Biochemical and Molecular Characterization of Musa sp. Cultured on Temporary Immersion Bioreactor

Author

Christopher A Sambolín Pérez, Rosalinda Aybar Batista, Sullymar Morales Marrero, Dinorah Andino Santiago, Axel Reyes Colón, Juan A Negron Berrios, Angel Núñez Marrero, and Alok Arun

Subjects
plant_sciences
Abstract

The genus Musa spp. contains commercially important fleshy fruit producing plants including plantains and bananas with a strong potential of providing food security and source of revenue to farmers. Occasionally, plantlets are often not available to fulfill the supply demand of farmers particularly in Caribbean region. Concerns with the quality of vegetative tissues along with the possibility of the transmission of phytopathogens makes availability of plantlets limited to farm-ers. Micropropagation of plantains offers an alternative to producing large number of in-vitro plantlets. However, conventional methods of micropropagation techniques require high produc-tion costs and are labor-intensive. Recently, Temporary Immersion Bioreactor (TIB) has emerged as an alternative to conventional micropropagation methods. Our work utilized SEM (Scanning Electron Microscope), molecular and biochemical tools (qRT-PCR and ICP-OES) to characterize and compare the morphological, elemental composition, and photosynthetic gene expression of plantains cultured on TIB. Additionally, morphological features of growth and propagation rates were analyzed for comparing outputs obtained from temporary immersion bioreactor with conventional micropropagation (CM) techniques. Results showed higher growth and multiplication rates for plantlets cultivated in TIB. Gene expression analysis of selected photosynthetic genes demonstrated high transcript abundance of phosphoenol pyruvate carboxylase (PEPC) in plantain tissues obtained by TIB. Elemental composition analysis showed higher content of iron in plantains grown in TIB suggesting a potential correlation with PEPC expression. These results demonstrate the potential of TIB to be an efficient method to produce healthy in-vitro plantains.

Published
2023

7. Mosaic Evolution of Molecular Pathways for Sex Pheromone Communication in a Butterfly

Author

Alok Arun, Christophe Klopp, Georges Lognay, Lucie Bastin-Héline, Gilles San Martin, Céline Noirot, Véronique Baumle, Patrícia Beldade, Bertanne Visser, Caroline M. Nieberding, Emmanuelle Jacquin-Joly, Nicolas Montagné, Repositório da Universidade de Lisboa, and UCL - SST/ELI/ELIB - Biodiversity

Subjects
Male, biology, Odorant binding, Mosaic evolution, media_common.quotation_subject, Neuropeptides, Bicyclus anynana, Insect, Moths, biology.organism_classification, Pheromones, olfactory communication, desaturase, reductase, odorant receptor, odorant binding protein, chemosensory protein, PBAN, phylogeny, Animal Communication, Mate choice, Phylogenetics, Evolutionary biology, Sex pheromone, Pheromone biosynthesis activating neuropeptide, Genetics, Animals, Female, Sex Attractants, Butterflies, Genetics (clinical), media_common
Abstract

Unraveling the origin of molecular pathways underlying the evolution of adaptive traits is essential for understanding how new lineages emerge, including the relative contribution of conserved, ancestral traits, and newly evolved, derived traits. Here, we investigated the evolutionary divergence of sex pheromone communication from moths (mostly nocturnal) to butterflies (mostly diurnal) that occurred ~98 million years ago. In moths, females typically emit pheromones to attract male mates, but in butterflies pheromones and used by females for mate choice. The molecular bases of sex pheromone communication are well understood in moths, but have remained virtually unexplored in butterflies. We used a combination of transcriptomics, real time qPCR, and phylogenetics, to identify genes involved in different steps of sex pheromone communication in the butterfly Bicyclus anynana. Our results show that the biosynthesis and reception of sex pheromones relies both on moth-specific gene families (reductases) and on more ancestral insect gene families (desaturases, olfactory receptors, odorant binding proteins). Interestingly, B. anynana further appears to use what was believed to be the moth-specific neuropeptide Pheromone Biosynthesis Activating Neuropeptide (PBAN) for regulation of sex pheromone production. Altogether, our results suggest that a mosaic pattern best explains how sex pheromone communication evolved in butterflies, with some molecular components derived from moths, and others conserved from more ancient insect ancestors. This is the first large-scale analysis of the genetic pathways underlying sex pheromone communication in a butterfly.

Published
2022

8. Micropropagation of Rare Scutellaria Havanensis Jacq. And Preliminary Studies on Antioxidant Capacity and Anti-cancer Potential

Author

Alok Arun, Brajesh N. Vaidya, Kamila Rivera Rivera, Nirmal Joshee, Juan A. Negrón Berríos, Lani Irvin, Yarelia Zavala Ortiz, and Samantha H Sherman

Subjects
Traditional medicine, biology, fungi, food and beverages, Cancer, biology.organism_classification, medicine.disease, plant_sciences, Trichome, Antioxidant capacity, Micropropagation, Polyphenol, Scutellaria, medicine
Abstract

We report the development of in vitro propagation protocols through adventitious shoot induction pathway for a rare and medicinal Scutellaria havanensis. In vitro propagation studies using nodal explants showed MS medium supplemented with 10µM 6-Benzylaminopurine induced highest number of adventitious shoots in a time dependent manner. A ten - day incubation was optimum for shoot bud induction as longer exposures resulted in hyperhydricity of the explants and shoots induced. We also report preliminary evidence of Agrobacterium tumefaciens EHA105 - mediated gene transfer transiently expressing of green fluorescent protein in this species. Transformation studies exhibited amenability of various explant tissues, internode being the most receptive. As the plant has medicinal value, research was carried out to evaluate its potential antioxidant capacity and the efficacy of methanolic leaf extracts in curbing the viability of human colorectal cancer cell line HCT116. Comparative total polyphenol, and flavonoid content measurement of fresh and air dried leaf extract revealed that the fresh leaf extracts contain higher total polyphenol and flavonoid content. The HCT 116 cell viability assessed by colorimetric assay using a 3-(4, 5-dimethyl-thiazol-2-yl)-2, 5-diphenyltetrazolium bromide, showed a steady growth inhibition after 24 hours of incubation. Scanning Electron Microscopy of leaf surface revealed high density of glandular and non-glandular trichomes. This research provides basis for the conservation of this rare plant and future phytochemical screening and clinical research.

Published
2021

9. Author response: Vision, challenges and opportunities for a Plant Cell Atlas

Author

Luis C. Romero, Ai My Luong, Jenny C Mortimer, Nicolas L. Taylor, Sergio Alan Cervantes-Pérez, David W. Ehrhardt, Yana Kazachkova, Adrien Burlaocot, Rajiv K. Tripathi, Alfredo Cruz-Ramírez, Nicholas J. Provart, Uwe John, Shou-Ling Xu, Renate A Weizbauer, Mathew G. Lewsey, José M. Palma, R. Glen Uhrig, Asela J. Wijeratne, Maria J. Harrison, William P Dwyer, Alexander T. Borowsky, Yuling Jiao, Kaushal Kumar Bhati, Edoardo Bertolini, Anna Stepanova, Francisco J. Corpas, Fabio Zanini, Pubudu P. Handakumbura, Dominique C. Bergmann, Devang Mehta, Saroj K Sah, Naomi Nakayama, Claire D McWhite, Jahed Ahmed, Dhruv Lavania, Gazala Ameen, Mather A Khan, Marc Libault, Gergo Palfalvi, Seung Y. Rhee, Laura E. Bartley, Vaishali Arora, Cesar L. Cuevas-Velazquez, Josh T. Cuperus, Benjamin Buer, Amir H. Ahkami, Lachezar A. Nikolov, Selena L Rice, Feng Zhao, Ronelle Roth, Ajay Kumar, Atique ur Rehman, Andrew Farmer, Maida Romera-Branchat, Zhi-Yong Wang, Tuan M Tran, Lydia-Marie Joubert, Le Liu, Julia Bailey-Serres, Fabio Gomez-Cano, Ramin Yadegari, Sanjay Joshi, James Whelan, Batthula Vijaya Lakshmi Vadde, Rachel Shahan, Houlin Yu, Bao-Hua Song, Andrey V Malkovskiy, Arun Kumar, Aaron J. Ogden, Javier Brumos, Xiaohong Zhuang, Oluwafemi Alaba, Harmanpreet Kaur, Tatsuya Nobori, Marisa S. Otegui, Peter H Denolf, Miguel Miñambres Martín, Sakil Mahmud, Tingting Xiang, Lisa I David, Justin W. Walley, Purva Karia, Maite Saura-Sanchez, Pankaj Kumar, Jamie Waese, Ansul Lokdarshi, Suryatapa Ghosh Jha, Sagar Kumar, Matthew M. S. Evans, Hai Ying Yuan, Rajveer Singh, Puneet Paul, Carly A Martin, Robert E. Jinkerson, Dianyi Liu, Rajdeep S. Khangura, Dae Kwan Ko, Tedrick Thomas Salim Lew, Jennifer A N Brophy, Ari Pekka Mähönen, Marija Vidović, Mark-Christoph Ott, Alok Arun, Pinky Agarwal, Pradeep Kumar, Alexandre P. Marand, R. Clay Wright, Moises Exposito-Alonso, Rosangela Sozzani, Tamas Varga, Luigi Di Costanzo, Shyam Solanki, Sixue Chen, Chien-Yuan Lin, Iain C. Macaulay, Tie Liu, Elsa H Quezada-Rodríguez, Trevor M. Nolan, Peter Denolf, Stefania Giacomello, Elizabeth S. Haswell, Nancy George, Noel Blanco-Touriñán, Bruno Contreras-Moreira, Benjamin J. Cole, Abhishek Joshi, Steven P. Briggs, Toshihiro Obata, Kerstin Kaufmann, Kenneth D. Birnbaum, Klaas J. van Wijk, Noah Fahlgren, Kamal Kumar Malukani, Ramesh Katam, Pingtao Ding, Mario A. Arteaga-Vazquez, Marcela K. Tello-Ruiz, Shao-shan Carol Huang, Sunil Kumar Kenchanmane Raju, Venura Herath, George W. Bassel, Christopher R. Anderton, Stefan de Folter, Gary Stacey, and Jie Zhu

Subjects
Engineering, Atlas (topology), business.industry, business, Data science
Published
2021

10. Vision, challenges and opportunities for a Plant Cell Atlas

Author

George W. Bassel, Claire D McWhite, Dhruv Lavania, Gazala Ameen, Christopher R. Anderton, Rajiv K. Tripathi, Maria J. Harrison, Josh T. Cuperus, Amir H. Ahkami, William P Dwyer, Bao-Hua Song, Fabio Zanini, Miguel Miñambres Martín, Atique ur Rehman, Cesar L. Cuevas-Velazquez, Ari Pekka Mähönen, Tamas Varga, Gergo Palfalvi, Andrew Farmer, Matthew M. S. Evans, Vaishali Arora, Uwe John, Mathew G. Lewsey, Dominique C. Bergmann, Selena L Rice, Mario A. Arteaga-Vazquez, Dae Kwan Ko, Tedrick Thomas Salim Lew, Jennifer A N Brophy, Jenny C Mortimer, Marc Libault, Bruno Contreras-Moreira, Benjamin J. Cole, Naomi Nakayama, Marcela K. Tello-Ruiz, Ronelle Roth, Laura E. Bartley, Tingting Xiang, Benjamin Buer, Shyam Solanki, Nicolas L. Taylor, Feng Zhao, Shao-shan Carol Huang, Alok Arun, Pinky Agarwal, Marisa S. Otegui, Arun Kumar, Marija Vidović, Pankaj Kumar, Aaron J. Ogden, Sagar Kumar, Puneet Paul, Sergio Alan Cervantes-Pérez, Purva Karia, Stefan de Folter, Kerstin Kaufmann, Gary Stacey, Le Liu, Robert E. Jinkerson, Javier Brumos, Harmanpreet Kaur, Tatsuya Nobori, David W. Ehrhardt, Francisco J. Corpas, Steven P. Briggs, James Whelan, Batthula Vijaya Lakshmi Vadde, Peter H Denolf, Tie Liu, Kamal Kumar Malukani, Elsa H Quezada-Rodríguez, Jahed Ahmed, Hai Ying Yuan, Rajveer Singh, Trevor M. Nolan, Ramesh Katam, Mather A Khan, Jamie Waese, Toshihiro Obata, Ramin Yadegari, Lachezar A. Nikolov, Seung Y. Rhee, Luis C. Romero, Ajay Kumar, Kenneth D. Birnbaum, Nicholas J. Provart, Tuan M Tran, Sakil Mahmud, Maida Romera-Branchat, Pradeep Kumar, Saroj K Sah, Ai My Luong, Alexandre P. Marand, R. Clay Wright, Yana Kazachkova, Moises Exposito-Alonso, Klaas J. van Wijk, Noah Fahlgren, Peter Denolf, Fabio Gomez-Cano, Houlin Yu, Luigi Di Costanzo, Adrien Burlaocot, Alfredo Cruz-Ramírez, Pingtao Ding, Dianyi Liu, Renate A Weizbauer, Suryatapa Ghosh Jha, Jie Zhu, Pubudu P. Handakumbura, Kaushal Kumar Bhati, Edoardo Bertolini, Anna Stepanova, Rachel Shahan, Lisa I David, Justin W. Walley, Lydia-Marie Joubert, Nancy George, Sanjay Joshi, José M. Palma, Rosangela Sozzani, Mark-Christoph Ott, Sixue Chen, Ansul Lokdarshi, Sunil Kumar Kenchanmane Raju, Chien-Yuan Lin, Iain C. Macaulay, Venura Herath, Noel Blanco-Touriñán, Rajdeep S. Khangura, Zhi-Yong Wang, Alexander T. Borowsky, Julia Bailey-Serres, Andrey V Malkovskiy, Xiaohong Zhuang, Oluwafemi Alaba, Yuling Jiao, Abhishek Joshi, Devang Mehta, Maite Saura-Sanchez, Carly A Martin, Stefania Giacomello, Elizabeth S. Haswell, Shou-Ling Xu, R. Glen Uhrig, Asela J. Wijeratne, National Science Foundation (US), Jha, S. G., Borowsky, A. T., Cole, B. J., Fahlgren, N., Farmer, A., Huang, S. C., Karia, P., Libault, M., Provart, N. J., Rice, S. L., Saura-Sanchez, M., Agarwal, P., Ahkami, A. H., Anderton, C. R., Briggs, S. P., Brophy, J. A., Denolf, P., Di Costanzo, L., Exposito-Alonso, M., Giacomello, S., Gomez-Cano, F., Kaufmann, K., Ko, D. K., Kumar, S., Malkovskiy, A. V., Nakayama, N., Obata, T., Otegui, M. S., Palfalvi, G., Quezada-Rodriguez, E. H., Singh, R., Uhrig, R. G., Waese, J., VAN WIJK, K., Wright, R. C., Ehrhardt, D. W., Birnbaum, K. D., Rhee, S. Y., Helsinki Institute of Life Science HiLIFE, and Institute of Biotechnology

Subjects
Life Sciences & Biomedicine - Other Topics, 0106 biological sciences, Engineering, chlamydomonas reinhardtii, Chloroplasts, Plant Cell Atla, 0601 Biochemistry and Cell Biology, maize, 01 natural sciences, Zea may, Plant science, Molecular level, cell biology, Plant Cell Atlas Consortium, Image Processing, Computer-Assisted, Biology (General), single-cell omic, 2. Zero hunger, 0303 health sciences, Atlas (topology), General Neuroscience, Agriculture, General Medicine, Plants, ARABIDOPSIS, C-4 PHOTOSYNTHESIS, Plant Cell Atlas, single-cell omics, Plant development, VOCABULARY, SYSTEMS BIOLOGY, Medicine, location-to-function, Life Sciences & Biomedicine, 4D imaging, QH301-705.5, DATABASE, Science, Plant Development, Translational research, Cellular level, Environmental stewardship, Zea mays, Chloroplast, General Biochemistry, Genetics and Molecular Biology, MECHANISMS, 03 medical and health sciences, Component (UML), Plant Cells, Biology, 030304 developmental biology, General Immunology and Microbiology, business.industry, Feature Article, Computational Biology, Plant, 15. Life on land, 11831 Plant biology, GENE, Data science, science forum, translational research, 13. Climate action, A. thaliana, PLASTIDS, Biochemistry and Cell Biology, business, GENERATION, 010606 plant biology & botany
Abstract

With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them., National Science Foundation 1916797 David W Ehrhardt, Kenneth D Birnbaum, Seung Yon Rhee; National Science Foundation 2052590 Seung Yon Rhee

Published
2021

11. Cambium-specific Transcriptome Analysis of Paulownia to Study the Molecular Impacts of Winter and Spring Seasons on Tree Growth

Author

Chhandak Basu, Umesh K. Reddy, Brajesh N. Vaidya, Thangasamy Saminathan, Nirmal Joshee, Alok Arun, and Zachary D. Perry

Subjects
chemistry.chemical_classification, Secondary growth, Paulownia, Biology, biology.organism_classification, Transcriptome, chemistry.chemical_compound, chemistry, Auxin, Paulownia elongata, Cytokinin, Botany, Lignin, Cambium
Abstract

Paulownia (Paulownia elongata) is a fast-growing, multipurpose deciduous hardwood species that grows in a wide range of temperatures from –30 °C to 45 °C. Seasonal cues influence the secondary growth of tree stems, including cambial activity, wood chemistry, and transition to latewood formation. In this study, ade novotranscriptome approach was conducted to identify the transcripts expressed in vascular cambial tissue from senescent winter and actively growing spring seasons. Illumina paired-end sequenced cambial transcriptome generated 297,049,842 clean reads which finally yielded 61,639 annotated unigenes. Based on non- redundant protein database analyses, Paulownia cambial unigenes shared highest homology (64.8%) withErythranthe guttata. A total of 35,471 unigenes resulted from KEGG annotation that were mapped to 128 pathways with metabolic pathways dominated among all. Additionally, DEG analysis showed that 2,688 and 7,411 genes were significantly upregulated and downregulated, respectively in spring compared to winter. Interestingly, quite a number of transcripts belonging to heat shock proteins were upregulated in spring season. RT-qPCR expression results of fifteen wood-forming candidate genes involved in hemicellulose, cellulose, lignin, auxin and cytokinin pathways showed that the hemicellulose genes (CSLC4, FUT1, AXY4, GATL1, andIRX19) were significantly upregulated in spring season tissues when compared to winter tissues. In contrast, lignin pathway genesCCR1andCAD1were upregulated in winter cambium. Finally, a transcriptome-wide marker analysis identified 11,338 Simple Sequence Repeat (SSRs). The AG/CT dinucleotide repeat predominately represented all SSRs. Altogether, the cambial transcriptomic analysis reported here highlights the molecular events of wood formation during winter and spring. The identification of candidate genes involved in the cambial growth provides a roadmap of wood formation in Paulownia and other trees for the seasonal growth variation.

Published
2020

14. Author response: Convergent recruitment of TALE homeodomain life cycle regulators to direct sporophyte development in land plants and brown algae

Author

Haiqin Yao, Komlan Avia, Martina Strittmatter, Delphine Scornet, Laurent Peres, Christelle Troadec, Nicolas Macaisne, Akira F. Peters, Abdelhafid Bendahmane, Alok Arun, Gabriel J Montecinos, Simon Bourdareau, J. Mark Cock, Agnieszka P. Lipinska, Olivier Godfroy, and Susana M. Coelho

Subjects
Brown algae, biology, Botany, Homeobox, Sporophyte, biology.organism_classification
Published
2019

15. Current Status and Future Prospects for Select Underutilized Medicinally Valuable Plants of Puerto Rico: A Case Study

Author

Lubana Shahin, Juan A. Negrón Berríos, Alok Arun, Prachi Tripathi, Ankush Sangra, and Richa Bajaj

Subjects
Geography, Agroforestry, Plant species, Medicinal plants
Abstract

In the last century, nearly all compounds of medicinal value were derived from naturally occurring compounds found in plants, bacteria, and fungi. Yet even today several interesting plant species with potential medicinal value remain underutilized and neglected. In a changing world, where unfavorable climatic and anthropogenic scenarios threaten natural vegetation across the globe, there is an urgent need to identify and investigate underutilized medicinal plants. Also, the utilization of such species should go hand in hand with their conservation. With the island territory of Puerto Rico as an example, we present a case for such underutilized medicinal plant species which could end up being the source of the next wonder drug for humanity. We also emphasize the need for sustainable utilization of such resources to go hand in hand with their conservation.

Published
2019

16. Convergent recruitment of life cycle regulators to direct sporophyte development in two eukaryotic supergroups

Author

Christelle Troadec, Akira F. Peters, Alok Arun, Martina Strittmatter, Nicolas Macaisne, Delphine Scornet, Olivier Godfroy, Gabriel J Montecinos, Komlan Avia, Susana M. Coelho, Simon Bourdareau, J. M. Cock, A. P. Lipinska, Abdelhafid Bendahmane, Yao H, Laurent Peres, Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Pathologie et virologie moléculaire (PVM (UMR_7151)), Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Diderot - Paris 7 (UPD7)

Subjects
0106 biological sciences, Gametophyte, 0303 health sciences, Lineage (genetic), biology, Archaeplastida, [SDV]Life Sciences [q-bio], Brown algae, Sporophyte, [SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology, Ectocarpus, biology.organism_classification, 01 natural sciences, 03 medical and health sciences, Multicellular organism, Evolutionary biology, life cycle, Gene, [SDV.BDD]Life Sciences [q-bio]/Development Biology, TALE homeodomain transcription factor, 030304 developmental biology, 010606 plant biology & botany, Chromalveolata
Abstract

Three amino acid loop extension homeodomain transcription factors (TALE HD TFs) act as life cycle regulators in green algae and land plants. In mosses these regulators are required for the deployment of the sporophyte developmental program. We demonstrate that mutations in either of two TALE HD TF genes, OUROBOROS or SAMSARA, in the brown alga Ectocarpus result in conversion of the sporophyte generation into a gametophyte. The OUROBOROS and SAMSARA proteins heterodimerise in a similar manner to TALE HD TF life cycle regulators in the green lineage. These observations demonstrate that TALE-HD-TF-based life cycle regulation systems have an extremely ancient origin, and that these systems have been independently recruited to regulate sporophyte developmental programs in at least two different complex multicellular eukaryotic supergroups, Archaeplastida and Chromalveolata.

Published
2018

17. Sequencing and De Novo Assembly of the Complete Chloroplast Genome of the Peruvian Carrot (Arracacia xanthorrhiza Bancroft)

Author

Alok Arun, Rosalinda Aybar Batista, Javier Santiago Alvarado, Juan A. Negrón Berríos, Diane Hinojosa López, Isaury Maldonado Torres, Vivek Kumar Raxwal, and María Margarita Meléndez

Subjects
0106 biological sciences, 0301 basic medicine, Whole genome sequencing, Eukaryotes, fungi, Sequence assembly, food and beverages, Biology, 01 natural sciences, Genome, DNA sequencing, food.food, Crop protection, Crop, 03 medical and health sciences, Arracacia xanthorrhiza, 030104 developmental biology, food, Chloroplast DNA, Botany, Genetics, Molecular Biology, 010606 plant biology & botany
Abstract

Arracacia xanthorrhiza is an important secondary food crop in South America and Puerto Rico. The lack of crop protection and improvement strategies leads to infections damaging the storage roots. Here, we report the annotated complete chloroplast genome sequence of A. xanthorrhiza as a step toward developing genomic resources for this crop.

Published
2017

18. Spectrum of chromosomal configurations in pollen mother cells ofRhoeo spathacea(Swartz) Stearn

Author

Koul Kuldeep Kumar, Ranjna Nagpal, and Alok Arun

Subjects
Chromosomal translocation, Mother cells, Biology, Ring (chemistry), medicine.disease_cause, Molecular biology, Chiasma, Meiosis, Pollen, Prophase I, Genetics, medicine, Metaphase i, General Agricultural and Biological Sciences
Abstract

Rhoeo spathacea is unusual in that its twelve chromosomes are involved in complex translocations that results in atypical meiosis with all chromosomes frequently joined end-to-end into a single ring. The detailed meiotic studies, for the first time, revealed that alignment of chromosomes into a ring and / or a chain begins at very early prophase I. However, the cells at diakinesis and metaphase I do not exclusively have a ring or a chain of 12 chromosomes. Instead, they carry a range of chain configurations formed due to slipping of the chiasmata off the pairing segments in complex structures. While in 57.61% cells, at diakinesis, a ring or a chain was observed, in the rest 2–7 chain configurations existed. Similarly, at metaphase I a ring of 12 chromosomes was observed in 33.87% cells whereas in 66.13 % cells 2–9 chain configurations existed. The various groups of chromosomes in cells at diakinesis generally did not show any specific orientation pattern. However, in 17.31% cells a disjunctional ...

Published
2011

19. Brown Algae

Author

Priyanka Verma, Alok Arun, and Dinabandhu Sahoo

Subjects
0106 biological sciences, 0303 health sciences, 03 medical and health sciences, 01 natural sciences, 030304 developmental biology, 010606 plant biology & botany
Published
2015

20. Selection and validation of reference genes for qRT-PCR expression analysis of candidate genes involved in olfactory communication in the butterfly Bicyclus anynana

Author

Caroline M. Nieberding, Véronique Baumle, Gaël Amelot, Alok Arun, and UCL - SST/ELI/ELIB - Biodiversity

Subjects
Male, Candidate gene, Molecular Sequence Data, lcsh:Medicine, Genes, Insect, Biology, Real-Time Polymerase Chain Reaction, QH301, Reference genes, Gene expression, Animals, Sex Attractants, lcsh:Science, Genetic Association Studies, Genetics, Multidisciplinary, Gene Expression Profiling, lcsh:R, Reproducibility of Results, Bicyclus anynana, Reference Standards, biology.organism_classification, Smell, Gene expression profiling, Real-time polymerase chain reaction, Female, Evolutionary ecology, lcsh:Q, RNA extraction, Butterflies, Software, Research Article
Abstract

Real-time quantitative reverse transcription PCR (qRT-PCR) is a technique widely used to quantify the transcriptional expression level of candidate genes. qRT-PCR requires the selection of one or several suitable reference genes, whose expression profiles remain stable across conditions, to normalize the qRT-PCR expression profiles of candidate genes. Although several butterfly species (Lepidoptera) have become important models in molecular evolutionary ecology, so far no study aimed at identifying reference genes for accurate data normalization for any butterfly is available. The African bush brown butterfly Bicyclus anynana has drawn considerable attention owing to its suitability as a model for evolutionary ecology, and we here provide a maiden extensive study to identify suitable reference gene in this species. We monitored the expression profile of twelve reference genes: eEF-1α, FK506, UBQL40, RpS8, RpS18, HSP, GAPDH, VATPase, ACT3, TBP, eIF2 and G6PD. We tested the stability of their expression profiles in three different tissues (wings, brains, antennae), two developmental stages (pupal and adult) and two sexes (male and female), all of which were subjected to two food treatments (food stress and control feeding ad libitum). The expression stability and ranking of twelve reference genes was assessed using two algorithm-based methods, NormFinder and geNorm. Both methods identified RpS8 as the best suitable reference gene for expression data normalization. We also showed that the use of two reference genes is sufficient to effectively normalize the qRT-PCR data under varying tissues and experimental conditions that we used in B. anynana. Finally, we tested the effect of choosing reference genes with different stability on the normalization of the transcript abundance of a candidate gene involved in olfactory communication in B. anynana, the Fatty Acyl Reductase 2, and we confirmed that using an unstable reference gene can drastically alter the expression profile of the target candidate genes.

Published
2015

21. Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida

Author

Tristan Barbeyron, Wilfrid Carré, Michael Katinka, Loraine Brillet, Klaus Valentin, Karine Labadie, Betina M. Porcel, Zofia Nehr, Francisco Cabello-Hurtado, Mirjam Czjzek, Benjamin Noel, Philippe Deschamps, Susana M. Coelho, John H. F. Bothwell, Pascal J. Lopez, Marek Eliáš, François Artiguenave, François-Yves Bouget, Thierry Tonon, Jean Weissenbach, Christophe Colleoni, Deirdre H. McLachlan, Ahmed A. Moustafa, Cécile Hervé, Olivier Panaud, Catherine Boyen, Jonas Collén, Antonios Zambounis, Frédéric Partensky, Cristian Chaparro, Ludovic Delage, Jose Fernandes Barbosa-Neto, Salvador Capella-Gutierrez, Bernard Kloareg, Nathalie Kowalczyk, Gaelle Samson, Gurvan Michel, Simon M. Dittami, Jean-Marc Aury, J. Mark Cock, Patrick Wincker, Agnès Groisillier, Pi Nyvall Collén, Bénédicte Charrier, Corinne Da Silva, Catherine Leblanc, Lionel Cladière, Alok Arun, Laurence Meslet-Cladiere, Claire M. M. Gachon, Sylvie Rousvoal, Kamel Jabbari, Stefan A. Rensing, Toni Gabaldón, Steven G. Ball, Aikaterini Symeonidi, Julie Poulain, Végétaux marins et biomolécules, Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-GOEMAR-Centre National de la Recherche Scientifique (CNRS), Procaryotes Phototrophes Marins = MArine Phototrophic Prokaryotes (MAPP), Adaptation et diversité en milieu marin (AD2M), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'Energie Atomique, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Department of Plant Physiology, Faculty of Sciences, Charles University [Prague] (CU), Belfast e-Science Centre [Belfast] (BESC), Queen's University [Belfast] (QUB), Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire océanologique de Banyuls (OOB), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Universitat Pompeu Fabra [Barcelona] (UPF), Center for Genomic Regulation (CRG-UPF), CIBER de Epidemiología y Salud Pública (CIBERESP), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Scottish Association for Marine Science (SAMS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Biology and Biotechnology Graduate Program, American University in Cairo, American University in Cairo, University of Freiburg [Freiburg], Freiburg Initiative in Systems Biology, Centre for Research and Technology Hellas (CERTH), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), MArine Phototrophic Prokaryotes (MAPP), Adaptation et diversité en milieu marin (ADMM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Charles University [Prague], Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Universitat Pompeu Fabra [Barcelona], Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut de Recherche pour le Développement (IRD), Institut de Recherche pour le Développement (IRD)-Institut Universitaire Européen de la Mer (IUEM), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Center for Research and Technology Hellas, Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Institut National de la Recherche Agronomique (INRA)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Observatoire océanologique de Banyuls (OOB), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), and Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Transposable element, Genome evolution, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Bacterial genome size, Biology, Chondrus, MESH: Base Sequence, MESH: RNA, Plant, Genes, Plant, 01 natural sciences, Genome, Evolution, Molecular, 03 medical and health sciences, MESH: Genes, Plant, 14. Life underwater, Gene, Genome size, MESH: Evolution, Molecular, 030304 developmental biology, Plant Proteins, Genetics, 0303 health sciences, Multidisciplinary, MESH: Molecular Sequence Data, Base Sequence, MESH: Plant Proteins, Archaeplastida, Biological Sciences, biology.organism_classification, MicroRNAs, RNA, Plant, MESH: MicroRNAs, MESH: Chondrus, 010606 plant biology & botany
Abstract

Red seaweeds are key components of coastal ecosystems and are economically important as food and as a source of gelling agents, but their genes and genomes have received little attention. Here we report the sequencing of the 105-Mbp genome of the florideophyte Chondrus crispus (Irish moss) and the annotation of the 9,606 genes. The genome features an unusual structure characterized by gene-dense regions surrounded by repeat-rich regions dominated by transposable elements. Despite its fairly large size, this genome shows features typical of compact genomes, e.g., on average only 0.3 introns per gene, short introns, low median distance between genes, small gene families, and no indication of large-scale genome duplication. The genome also gives insights into the metabolism of marine red algae and adaptations to the marine environment, including genes related to halogen metabolism, oxylipins, and multicellularity (microRNA processing and transcription factors). Particularly interesting are features related to carbohydrate metabolism, which include a minimalistic gene set for starch biosynthesis, the presence of cellulose synthases acquired before the primary endosymbiosis showing the polyphyly of cellulose synthesis in Archaeplastida, and cellulases absent in terrestrial plants as well as the occurrence of a mannosylglycerate synthase potentially originating from a marine bacterium. To explain the observations on genome structure and gene content, we propose an evolutionary scenario involving an ancestral red alga that was driven by early ecological forces to lose genes, introns, and intergenetic DNA; this loss was followed by an expansion of genome size as a consequence of activity of transposable elements.

Published
2013

22. Brown algae as a model for plant organogenesis

Author

Kenny A, Bogaert, Alok, Arun, Susana M, Coelho, and Olivier, De Clerck

Subjects
Organogenesis, Phaeophyta
Abstract

Brown algae are an extremely interesting, but surprisingly poorly explored, group of organisms. They are one of only five eukaryotic lineages to have independently evolved complex multicellularity, which they express through a wide variety of morphologies ranging from uniseriate branched filaments to complex parenchymatous thalli with multiple cell types. Despite their very distinct evolutionary history, brown algae and land plants share a striking amount of developmental features. This has led to an interest in several aspects of brown algal development, including embryogenesis, polarity, cell cycle, asymmetric cell division and a putative role for plant hormone signalling. This review describes how investigations using brown algal models have helped to increase our understanding of the processes controlling early embryo development, in particular polarization, axis formation and asymmetric cell division. Additionally, the diversity of life cycles in the brown lineage and the emergence of Ectocarpus as a powerful model organism, are affording interesting insights on the molecular mechanisms underlying haploid-diploid life cycles. The use of these and other emerging brown algal models will undoubtedly add to our knowledge on the mechanisms that regulate development in multicellular photosynthetic organisms.

Published
2013

23. Non-cell autonomous regulation of life cycle transitions in the model brown alga Ectocarpus

Author

Akira F. Peters, Susana M. Coelho, Alok Arun, Nick T. Peters, J. Mark Cock, Delphine Scornet, Végétaux marins et biomolécules, Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-GOEMAR-Centre National de la Recherche Scientifique (CNRS), Department of Biology [Utah], University of Utah, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Marine Biological Association Laboratory (MBA Laboratory), Marine Biological Association of the UK, Bezhin Rosko, Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Physiology, [SDV]Life Sciences [q-bio], MESH: Benzenesulfonates, Plant Science, Phaeophyta, MESH: Germ Cells, Plant, 01 natural sciences, Models, Biological, MESH: Genetic Loci, 03 medical and health sciences, Botany, Regeneration, 030304 developmental biology, Gametophyte, 0303 health sciences, biology, MESH: Culture Media, Conditioned, Ectocarpus siliculosus, Protoplasts, Benzenesulfonates, MESH: Models, Biological, MESH: Regeneration, Sporophyte, MESH: Phaeophyta, Ectocarpus, MESH: Protoplasts, biology.organism_classification, Multicellular organism, Evolutionary biology, Genetic Loci, Culture Media, Conditioned, Alternation of generations, Ploidy, Germ Cells, Plant, Reprogramming, 010606 plant biology & botany
Abstract

International audience; The model brown alga Ectocarpus has a haploid-diploid life cycle, involving alternation between two independent multicellular generations, the gametophyte and the sporophyte. Recent work has shown that alternation of generations is not determined by ploidy but is rather under genetic control, involving at least one master regulatory locus, OUROBOROS (ORO). Using cell biology approaches combined with measurements of generation-specific transcript abundance we provide evidence that alternation of generations can also be regulated by non-cell autonomous mechanisms. The Ectocarpus sporophyte produces a diffusible factor that causes major developmental reprogramming in gametophyte cells. Cells become resistant to reprogramming when the cell wall is synthetized, suggesting that the cell wall may play a role in locking an individual into the developmental program that has been engaged. A functional ORO gene is necessary for the induction of the developmental switch. Our results highlight the role of the cell wall in maintaining the differentiated generation stage once the appropriate developmental program has been engaged and also indicate that ORO is a key member of the developmental pathway triggered by the sporophyte factor. Alternation between gametophyte and sporophyte generations in Ectocarpus is surprisingly labile, perhaps reflecting an adaptation to the variable seashore environment inhabited by this alga.

Published
2013

24. Genomics of brown algae: current advances and future prospects

Author

Susana M. Coelho, Martina Strittmatter, Olivier Godfroy, J. Mark Cock, Akira F. Peters, Nicolas Macaisne, Alok Arun, Station biologique de Roscoff, Centre National de la Recherche Scientifique (CNRS), and Bezhin Rosko

Subjects
0106 biological sciences, genome sequence, [SDV]Life Sciences [q-bio], ved/biology.organism_classification_rank.species, Genomics, brown algae, 01 natural sciences, Biochemistry, Genome, 03 medical and health sciences, Genetics, 14. Life underwater, Model organism, Molecular Biology, Organism, 030304 developmental biology, Whole genome sequencing, 0303 health sciences, biology, ved/biology, Ecology, Ectocarpus siliculosus, Ectocarpus, biology.organism_classification, Brown algae, Evolutionary biology, 010606 plant biology & botany, biotechnology
Abstract

International audience; The analysis of the complete genome sequence of the filamentous brown alga Ectocarpus provided many new insights into brown algal biology and has improved our understanding of how this organism has adapted to its seashore environment. Since the publication of the genome sequence in 2010, numerous studies have continued the analysis of the constituent genes or have combined genome data with experimental work, allowing progress in several key areas, including metabolism and reproductive biology. Ectocarpus will continue to be exploited as a model organism in future years, but genomic approaches should also be extended to additional brown algal species in order to fully exploit the diversity of this phylogenetic group and to facilitate the application of new knowledge to economically important seaweeds such as kelps.

Published
2012

25. Genetic regulation of life cycle transitions in the brown alga Ectocarpus

Author

Gildas Le Corguillé, J. Mark Cock, Susana M. Coelho, Akira F. Peters, Olivier Godfroy, Alok Arun, Station biologique de Roscoff, Centre National de la Recherche Scientifique (CNRS), and Bezhin Rosko

Subjects
Phaeophyceae, homeotic mutation, [SDV]Life Sciences [q-bio], initial cell polarization, Plant Science, Biology, brown algae, Genes, Plant, Phaeophyta, Evolution, Molecular, life cycle, parthenogenesis, gametophyte, ComputingMilieux_MISCELLANEOUS, Organism, Gametophyte, initial cell polarisation, Ecology, Sporophyte, Ectocarpus, multicellularity, biology.organism_classification, Article Addendum, Multicellular organism, sporophyte, Evolutionary biology, Mutation (genetic algorithm), Mutation, Ectocarpus siliculosus, Biological dispersal, Adaptation, Germ Cells, Plant
Abstract

The life cycle of an organism is one of its most elemental features, underpinning a broad range of phenomena including developmental processes, reproductive fitness, mode of dispersal and adaptation to the local environment. Life cycle modification may have played an important role during the evolution of several eukaryotic groups, including the terrestrial plants. Brown algae are potentially interesting models to study life cycle evolution because this group exhibits a broad range of different life cycles. Currently, life cycle studies are focused on the emerging brown algal model Ectocarpus. Two life cycle mutants have been described in this species, both of which cause the sporophyte generation to exhibit gametophyte characteristics. The ouroboros mutation is particularly interesting because it induces complete conversion of the sporophyte generation into a functional, gamete-producing gametophyte, a class of mutation that has not been described so far in other systems. Analysis of Ectocarpus life cycle mutants is providing insights into several life-cycle-related processes including parthenogenesis, symmetric/asymmetric initial cell divisions and sex determination.

Published
2011

26. OUROBOROS is a master regulator of the gametophyte to sporophyte life cycle transition in the brownalga Ectocarpus

Author

Akira F. Peters, J. Mark Cock, Susana M. Coelho, Alok Arun, Olivier Godfroy, Gildas Le Corguillé, Laboratoire de Biologie Intégrative des Modèles Marins ( LBI2M ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), Station biologique de Roscoff [Roscoff] ( SBR ), Végétaux marins et biomolécules ( UMR7139 ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -GOEMAR-Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Végétaux marins et biomolécules, Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-GOEMAR-Centre National de la Recherche Scientifique (CNRS), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Mutant, Locus (genetics), Haploidy, Phaeophyta, 01 natural sciences, 03 medical and health sciences, RNA, Messenger, Oligonucleotide Array Sequence Analysis, 030304 developmental biology, Gametophyte, Genetics, 0303 health sciences, Multidisciplinary, Base Sequence, biology, Reverse Transcriptase Polymerase Chain Reaction, Ectocarpus siliculosus, Homozygote, Gene Expression Regulation, Developmental, Sporophyte, [SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology, Ectocarpus, Biological Sciences, biology.organism_classification, Diploidy, Phenotype, [ SDV.BDLR ] Life Sciences [q-bio]/Reproductive Biology, Mutation, Germ Cells, Plant, Ploidy, Homeotic gene, 010606 plant biology & botany
Abstract

The brown alga Ectocarpus siliculosus has a haploid–diploid life cycle that involves an alternation between two distinct generations, the sporophyte and the gametophyte. We describe a mutant, ouroboros ( oro ), in which the sporophyte generation is converted into a functional, gamete-producing gametophyte. The life history of the mutant thus consists of a continuous reiteration of the gametophyte generation. The oro mutant exhibited morphological features typical of the gametophyte generation and accumulated transcripts of gametophyte generation marker genes. Genetic analysis showed that oro behaved as a single, recessive, Mendelian locus that was unlinked to the IMMEDIATE UPRIGHT locus, which has been shown to be necessary for full expression of the sporophyte developmental program. The data presented here indicate that ORO is a master regulator of the gametophyte-to-sporophyte life cycle transition and, moreover, that oro represents a unique class of homeotic mutation that results in switching between two developmental programs that operate at the level of the whole organism.

Published
2011

27. Convergent recruitment of TALE homeodomain life cycle regulators to direct sporophyte development in land plants and brown algae

Author

Simon Bourdareau, Gabriel J Montecinos, Abdelhafid Bendahmane, Olivier Godfroy, Haiqin Yao, Susana M. Coelho, Christelle Troadec, Nicolas Macaisne, Alok Arun, J. Mark Cock, Agnieszka P. Lipinska, Laurent Peres, Komlan Avia, Delphine Scornet, Martina Strittmatter, Akira F. Peters, Arun, Alok, Coelho, Susana M., Cock, J. Mark, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Bezhin Rosko, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique, Agence Nationale de la Recherche [ANR-10-BLAN-1727, ANR-10-BTBR-04-01, ANR-10-LABX-40], Interreg Program France (Channel)-England, University Pierre and Marie Curie, European Commission European Erasmus Mundus program, China Scholarship Council, European Research Council ERC-SEXYPARTH, European Project: 638240,H2020,ERC-2014-STG,SEXSEA(2015), and Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)

Subjects
0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Plant Biology, 01 natural sciences, Gene Expression Regulation, Plant, life cycle, Biology (General), TALE homeodomain transcription factor, Plant Proteins, Gametophyte, biology, Archaeplastida, General Neuroscience, Sporophyte, General Medicine, Ectocarpus, sporophyte development, Phenotype, Medicine, stramenopiles, Protein Binding, Research Article, QH301-705.5, Science, Phaeophyta, brown algae, General Biochemistry, Genetics and Molecular Biology, Ectocarpus sp, Evolution, Molecular, 03 medical and health sciences, Protein Domains, Amino Acid Sequence, RNA, Messenger, Chromalveolata, Homeodomain Proteins, General Immunology and Microbiology, biology.organism_classification, Brown algae, Multicellular organism, 030104 developmental biology, Evolutionary biology, Mutation, Embryophyta, Homeobox, Other, Transcription Factors, 010606 plant biology & botany
Abstract

Three amino acid loop extension homeodomain transcription factors (TALE HD TFs) act as life cycle regulators in green algae and land plants. In mosses these regulators are required for the deployment of the sporophyte developmental program. We demonstrate that mutations in either of two TALE HD TF genes, OUROBOROS or SAMSARA, in the brown alga Ectocarpus result in conversion of the sporophyte generation into a gametophyte. The OUROBOROS and SAMSARA proteins heterodimerise in a similar manner to TALE HD TF life cycle regulators in the green lineage. These observations demonstrate that TALE-HD-TF-based life cycle regulation systems have an extremely ancient origin, and that these systems have been independently recruited to regulate sporophyte developmental programs in at least two different complex multicellular eukaryotic supergroups, Archaeplastida and Chromalveolata., eLife digest Brown algae and land plants are two groups of multicellular organisms that have been evolving independently for over a billion years. Their last common ancestor is thought to have existed as a single cell; then, complex multicellular organisms would have appeared separately in each lineage. Comparing brown algae and land plants therefore helps us understand the rules that guide how multicellular organisms evolve from single-celled ancestors. During their life cycles, both brown algae and land plants alternate between two multicellular forms: the gametophyte and the sporophyte. The gametophyte develops sexually active reproductive cells, which, when they merge, create the sporophyte. In turn, spores produced by the sporophyte give rise to the gametophyte. Specific developmental programs are deployed at precise points in the life cycle to make either a sporophyte or a gametophyte. Two proteins known as TALE HD transcription factors help to control the life cycle of single-celled algae related to land plants. Similar proteins are also required for the sporophyte to develop at the right time in land plants known as mosses. This suggests that, when multicellular organisms emerged in this lineage, life cycle TALE HD transcription factors were recruited to orchestrate the development of the sporophyte. However, it was not clear whether TALE HD transcription factors play equivalent roles in other groups, such as brown algae. To address this question, Arun, Coelho et al. examined two mutants of the brown alga Ectocarpus, which produce gametophytes when the non-mutated alga would have made sporophytes. Genetic analyses revealed that these mutated brown algae carried changes in two genes that encode TALE HD transcription factors, indicating that these proteins also regulate the formation of sporophytes in brown algae. Taken together, the results suggest that TALE HD transcription factors were originally tasked with controlling life cycles, and then have been independently harnessed in both land plants and brown algae to govern the formation of sporophytes. This means that, regardless of lineage, the same fundamental forces may be shaping the evolutionary paths that lead to multicellular organisms. Proteins similar to TALE HD transcription factors also regulate life cycles in other groups such as fungi and social amoebae, which indicates that their role is very ancient. It now remains to be explored whether such proteins control life cycles and developmental programs in other multicellular organisms, such as animals.

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28. Development of an electronic sensor for engine exhaust particulate measurements

Author

Warey, Alok Arun

Abstract

A new electronic sensor has been developed to measure the time-resolved concentration of carbonaceous particulate matter (PM) emitted in engine exhaust. The sensor is approximately the size of a standard automotive spark-plug or lambda sensor and can be mounted directly in the engine exhaust. It consists of a pair of closely spaced electrically isolated electrodes that protrude into the exhaust flow. One electrode is given a voltage bias of approximately1000 V while the other is the signal electrode. The sensor is capable of providing cycle-resolved feedback on the carbonaceous PM concentration in the exhaust to the engine control unit (ECU), thereby enabling real-time control of engine operating parameters. The sensor was tested in exhaust flows from a single cylinder diesel engine and from a steady-state acetylene diffusion flame in a flow tunnel. Steady-state engine measurements were made over a range of speed and load conditions while transient measurements were performed during engine start-ups and accelerations. The sensor response was compared to an opacity meter, gravimetric filter measurements, an aerodynamic particle sizer and a light scattering nephelometer. The output of the sensor compared well with exhaust opacity for the transient measurements and to filter mass loading for the steady-state tests. Various parameters that affect the performance of the electronic sensor were studied. Parameters considered included sensor electrode length, diameter, electrode spacing, applied bias voltage, bulk flow velocity across the sensor electrodes, and the concentration of carbonaceous particulate matter in engine exhaust. The sensor signal varied linearly with the carbon mass concentration in the exhaust, the applied bias voltage and electrode length; it varied exponentially with the flow velocity, and had an inverse power dependence on the spacing between the electrodes. Electrode diameter did not have a significant effect on the sensor signal. A correlation was developed to predict the sensor signal under any engine operating condition and values of these parameters. Based on the experimental data a hypothesis explaining the physical mechanism governing sensor behavior, regarding the charge transport between the two electrodes of the sensor, was proposed. A 1-D drift-diffusion model was developed to support this hypothesis.

Published
2005

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