Retinoic acid receptor assembly dynamics governs dual functions in cochlear organogenesis Saikat Chakraborty, Shuze Wang, Jack Ruhala, Brett Mehling, Jie Liu, Joerg Waldhaus Proceedings of the National Academy of Sciences of the United States of America, 2025 Retinoic acid (RA) is a morphogen that contributes to inner ear development. Gain and loss of function experiments have indicated retinoic acid’s critical role in cochlear hair cell development. However, the underlying molecular mechanisms are unclear. Here, we hypothesized that RA receptor alpha (RARA) has a dual role in cochlear organogenesis: First, during embryonic development, in the presence of RA, RARA functions as a transcriptional activator that induces prosensory gene expression in progenitor cells and supports differentiation of the organ of Corti; later during postnatal development, when RA is absent, the function of RARA switches, thereby repressing prosensory genes in postnatal hair cells and hindering trans-differentiation into supporting cells. This hypothesis was supported by demonstration that RARA forms a complex with either the coactivator NCOA1 or the corepressor NCOR1 depending on the developmental stage. In addition, modulation of RA levels was found to govern recruitment of the coactivator and corepressor to the RARA complex, and the expression of prosensory genes was validated to depend on RARA complex composition. Together, our results provide insights supporting the potential of harnessing RA signaling to induce prosensory progenitors in stem cell–based strategies for hearing loss.
Simple detection methods for antinutritive factor β-ODAP present in Lathyrus sativus L. by high pressure liquid chromatography and thin layer chromatography Bidisha Ghosh, Joy Mitra, Saikat Chakraborty, Jagannath Bhattacharyya, Anirban Chakraborty, Soumitra Kumar Sen, Muniasamy Neerathilingam Plos One, 2015 Lathyrus sativus L. (Grass pea) is the source for cheap and nutritious food choice in drought and famine susceptible zones in greater part of North India and Africa. The non-protein amino acid β-N-oxalyl-L-α,β-diaminopropionic acid (β-ODAP) has been known for decades for its potent neurotoxic effect, causing irreversible neurodegenerative disease “neurolathyrism”, present in both seed and leaf of Lathyrus sativus L. and other species in varying proportions. It is crucial to establish a rapid as well as reliable detection methodology for β-ODAP content in various Lathyrus plants. Currently available HPLC based methods involve multi-step derivatization of the sample. To overcome this, we have developed β-ODAP analysis method by HPLC without any prior derivatization. This method is statistically significant in the range of 2 to 100μg/ml and exhibited linear response with r 2 > 0.99. Limit of detection and quantitation of the later method was determined to be 5.56 μg/ml and 16.86 μg/ml, respectively. In addition to this, a TLC based method has also been developed. The limit of detection of β-ODAP is 0.6μg and for its substrate, L-1,2-diaminopropionic acid is 5μg. Both HPLC and TLC methods were validated by conducting in-vitro bioconversion test to detect the presence of biocatalyst in plant extract. This method is economical, rapid and simple.
Anther-Specific ß-1, 3-Glucanases 54 in Plant Male Sterility: Insights and Applications MK Samanta, A Banerjee, S Chakraborty Research and Innovations in Industrial and Marine Biotechnology: A Circular … , 2026 2026
Maternal CENP-C restores centromere symmetry in mammalian zygotes to ensure proper chromosome segregation CA Tower, G Manske, EL Ferrell, DN Anbarci, K Jorgensen, B Ma, ... Developmental Cell, 1-18 , 2025 2025 Citations: 3
Chromatin Modifier HMGA2 Links Embryonic Patterning to Tonotopic Function of the Cochlea S Chakraborty, L Cassinotti, J Ruhala, O Deb, G Corfas, J Waldhaus. https://www.ssrn.com/index.cfm/en/ , 2025 2025
Retinoic acid receptor assembly dynamics governs dual functions in cochlear organogenesis S Chakraborty, S Wang, J Ruhala, B Mehling, J Liu, J Waldhaus. Proceedings of the National Academy of Sciences of the United States of … , 2025 2025
3D reconstruction of the mouse cochlea from scRNA-seq data suggests morphogen-based principles in apex-to-base specification S Wang, S Chakraborty, Y Fu, MP Lee, J Liu, J Waldhaus Developmental cell 59 (12), 1538-1552. e6 , 2024 2024 Citations: 10
Equalizing epigenetically imprinted centromeres in early mammalian embryos G Manske, K Jorgensen, B Ma, M Aboelenain, C Tower, S Chakraborty, ... bioRxiv, 2022.10. 27.514094 , 2022 2022 Citations: 5
Tissue specific expression and in-silico characterization of a putative cysteine synthase gene from Lathyrus sativus L. S Chakraborty, J Mitra, MK Samanta, N Sikdar, J Bhattacharyya, A Manna, ... www.elsevier.com/locate/gep 27, 128-134 , 2018 2018 Citations: 11
Functional analysis of a rice tapetum specific (RTS) gene promoter variant identified in rice cultivar IR64 N Sikdar, A Chakraborty, J Bhattacharyya, S Chakraborty, BR Pati, ... Oryza 54 (2), 125-134 , 2017 2017 Citations: 2
A rapid and efficient protocol for in vitro plant regeneration of Lathyrus sativus L. (Grass pea) through multiple shooting S Chakraborty, J Bhattacharyya, A Manna, N Sikdar, A Chakraborty, ... International Journal of Current Research 8 (11), 41556-4156 , 2016 2016 Citations: 1
Marker-free transgenic rice expressing the vegetative insecticidal protein (Vip) of Bacillus thuringiensis shows broad insecticidal properties S Pradhan, A Chakraborty, N Sikdar, S Chakraborty, J Bhattacharyya, ... Planta 244 (4), 78 , 2016 2016 Citations: 26
Genetic transformation of cultivated sesame (Sesamum indicum L. cv Rama) through particle bombardment using 5-day-old apical, meristematic tissues of germinating seedlings J Bhattacharyya, A Chakraborty, J Mitra, S Chakraborty, S Pradhan, ... Plant Cell, Tissue and Organ Culture (PCTOC) 123, 455–466 , 2015 2015 Citations: 13
Transgenic expression of an unedited mitochondrial orfB gene product from wild abortive (WA) cytoplasm of rice (Oryza sativa L.) generates male sterility in fertile rice lines A Chakraborty, J Mitra, J Bhattacharyya, S Pradhan, N Sikdar, S Das, ... Planta 241 (Issue 6), pp 1463–1479 , 2015 2015 Citations: 29
PCR-based diagnostic protocol for orfB gene containing transgenic nuclear male sterile rice lines E Pandit, DP Mohanty, SR Barik, SP Mohanty, N Sikder, S Chakraborty, ... ORYZA-An International Journal on Rice 52 (4), 245-250 , 2015 2015
Simple Detection Methods for Antinutritive Factor β-ODAP Present in Lathyrus sativus L. by High Pressure Liquid Chromatography and Thin Layer Chromatography B Ghosh, J Mitra, S Chakraborty, J Bhattacharyya, A Chakraborty, SK Sen, ... PLOS One 10 (0140649), 1371 , 2015 2015 Citations: 16
Genetic transformation of cultivated jute (Corchorus capsularis L.) by particle bombardment using apical meristem tissue and development of stable transgenic plant JBACSRSPJMMCAMNSSCSKSE author PCTOC 121 (2), 311–32 , 2015 2015 Citations: 31
MOST CITED SCHOLAR PUBLICATIONS
Genetic transformation of cultivated jute (Corchorus capsularis L.) by particle bombardment using apical meristem tissue and development of stable transgenic plant JBACSRSPJMMCAMNSSCSKSE author PCTOC 121 (2), 311–32 , 2015 2015 Citations: 31
Transgenic expression of an unedited mitochondrial orfB gene product from wild abortive (WA) cytoplasm of rice (Oryza sativa L.) generates male sterility in fertile rice lines A Chakraborty, J Mitra, J Bhattacharyya, S Pradhan, N Sikdar, S Das, ... Planta 241 (Issue 6), pp 1463–1479 , 2015 2015 Citations: 29
Marker-free transgenic rice expressing the vegetative insecticidal protein (Vip) of Bacillus thuringiensis shows broad insecticidal properties S Pradhan, A Chakraborty, N Sikdar, S Chakraborty, J Bhattacharyya, ... Planta 244 (4), 78 , 2016 2016 Citations: 26
Simple Detection Methods for Antinutritive Factor β-ODAP Present in Lathyrus sativus L. by High Pressure Liquid Chromatography and Thin Layer Chromatography B Ghosh, J Mitra, S Chakraborty, J Bhattacharyya, A Chakraborty, SK Sen, ... PLOS One 10 (0140649), 1371 , 2015 2015 Citations: 16
Genetic transformation of cultivated sesame (Sesamum indicum L. cv Rama) through particle bombardment using 5-day-old apical, meristematic tissues of germinating seedlings J Bhattacharyya, A Chakraborty, J Mitra, S Chakraborty, S Pradhan, ... Plant Cell, Tissue and Organ Culture (PCTOC) 123, 455–466 , 2015 2015 Citations: 13
Tissue specific expression and in-silico characterization of a putative cysteine synthase gene from Lathyrus sativus L. S Chakraborty, J Mitra, MK Samanta, N Sikdar, J Bhattacharyya, A Manna, ... www.elsevier.com/locate/gep 27, 128-134 , 2018 2018 Citations: 11
3D reconstruction of the mouse cochlea from scRNA-seq data suggests morphogen-based principles in apex-to-base specification S Wang, S Chakraborty, Y Fu, MP Lee, J Liu, J Waldhaus Developmental cell 59 (12), 1538-1552. e6 , 2024 2024 Citations: 10
Equalizing epigenetically imprinted centromeres in early mammalian embryos G Manske, K Jorgensen, B Ma, M Aboelenain, C Tower, S Chakraborty, ... bioRxiv, 2022.10. 27.514094 , 2022 2022 Citations: 5
Maternal CENP-C restores centromere symmetry in mammalian zygotes to ensure proper chromosome segregation CA Tower, G Manske, EL Ferrell, DN Anbarci, K Jorgensen, B Ma, ... Developmental Cell, 1-18 , 2025 2025 Citations: 3
Functional analysis of a rice tapetum specific (RTS) gene promoter variant identified in rice cultivar IR64 N Sikdar, A Chakraborty, J Bhattacharyya, S Chakraborty, BR Pati, ... Oryza 54 (2), 125-134 , 2017 2017 Citations: 2
A rapid and efficient protocol for in vitro plant regeneration of Lathyrus sativus L. (Grass pea) through multiple shooting S Chakraborty, J Bhattacharyya, A Manna, N Sikdar, A Chakraborty, ... International Journal of Current Research 8 (11), 41556-4156 , 2016 2016 Citations: 1
Anther-Specific ß-1, 3-Glucanases 54 in Plant Male Sterility: Insights and Applications MK Samanta, A Banerjee, S Chakraborty Research and Innovations in Industrial and Marine Biotechnology: A Circular … , 2026 2026
Chromatin Modifier HMGA2 Links Embryonic Patterning to Tonotopic Function of the Cochlea S Chakraborty, L Cassinotti, J Ruhala, O Deb, G Corfas, J Waldhaus. https://www.ssrn.com/index.cfm/en/ , 2025 2025
Retinoic acid receptor assembly dynamics governs dual functions in cochlear organogenesis S Chakraborty, S Wang, J Ruhala, B Mehling, J Liu, J Waldhaus. Proceedings of the National Academy of Sciences of the United States of … , 2025 2025
PCR-based diagnostic protocol for orfB gene containing transgenic nuclear male sterile rice lines E Pandit, DP Mohanty, SR Barik, SP Mohanty, N Sikder, S Chakraborty, ... ORYZA-An International Journal on Rice 52 (4), 245-250 , 2015 2015
