@article{kareem_plant_2026,
	title = {Plant regeneration: {From} activation to fate determination},
	volume = {94},
	issn = {1369-5266},
	shorttitle = {Plant regeneration},
	url = {https://www.sciencedirect.com/science/article/pii/S1369526626001020},
	doi = {10.1016/j.pbi.2026.102959},
	abstract = {Plants exhibit diverse regeneration strategies to heal wounds, regrow organs, and clonally propagate. These regeneration strategies depend on inductive cues such as wounding, stress or hormones initiating cell division and cell differentiation. However, wounding activates both regeneration and defence responses, and it has become clear that plants actively decide when to regenerate and what to regenerate. By integrating cell wall, hormonal, mechanical and environmental cues, plants can initiate and shape diverse regeneration outcomes such as callus formation, root regeneration, grafting and shoot formation. Here, we discuss the latest developments in how plants activate regeneration and establish a multitude of diverse regeneration outcomes. We focus on the diversity of regeneration, the trade-off between defence and regeneration, the role of signalling in fate determination and how external cues promote regeneration plasticity. Such knowledge has implications for better understanding the adaptive relevance of regeneration and for modifying fate outcomes to enhance biotechnological applications of plant regeneration.},
	urldate = {2026-09-08},
	journal = {Current Opinion in Plant Biology},
	author = {Kareem, Abdul and Melnyk, Charles W.},
	month = dec,
	year = {2026},
	pages = {102959},
}

Plants exhibit diverse regeneration strategies to heal wounds, regrow organs, and clonally propagate. These regeneration strategies depend on inductive cues such as wounding, stress or hormones initiating cell division and cell differentiation. However, wounding activates both regeneration and defence responses, and it has become clear that plants actively decide when to regenerate and what to regenerate. By integrating cell wall, hormonal, mechanical and environmental cues, plants can initiate and shape diverse regeneration outcomes such as callus formation, root regeneration, grafting and shoot formation. Here, we discuss the latest developments in how plants activate regeneration and establish a multitude of diverse regeneration outcomes. We focus on the diversity of regeneration, the trade-off between defence and regeneration, the role of signalling in fate determination and how external cues promote regeneration plasticity. Such knowledge has implications for better understanding the adaptive relevance of regeneration and for modifying fate outcomes to enhance biotechnological applications of plant regeneration.

@article{kareem_tmo5_2025,
	title = {{TMO5} regulates {PIN1} polarity convergence and organogenesis downstream of {MONOPTEROS} in the {Arabidopsis} shoot},
	volume = {152},
	issn = {0950-1991},
	url = {https://doi.org/10.1242/dev.205255},
	doi = {10.1242/dev.205255},
	abstract = {Plants continuously produce lateral organs, such as leaves and flowers, from the shoot apical meristem (SAM). This process is guided by the accumulation of the plant hormone auxin and the polar localization of the efflux protein PIN-FORMED1 (PIN1). The transcription factor MONOPTEROS (MP) plays a crucial role in orienting PIN1 polarity, thereby facilitating auxin-driven organogenesis. In this study, we investigate genes downstream of MP that may regulate PIN1 polarity and organogenesis, discovering that the downstream vascular transcription factor TMO5 can promote PIN1 polarity convergence non-cell-autonomously and that TMO5 and its family members promote organ initiation in the SAM. By examining the role of auxin and cytokinin downstream of these genes, we provide evidence that the TMO5-like genes control PIN1 polarity and drive organogenesis by coordinating multiple hormonal signalling pathways.},
	number = {24},
	urldate = {2026-09-07},
	journal = {Development},
	author = {Kareem, Abdul and Ohno, Carolyn and Heisler, Marcus G.},
	month = dec,
	year = {2025},
	pages = {dev205255},
}

Plants continuously produce lateral organs, such as leaves and flowers, from the shoot apical meristem (SAM). This process is guided by the accumulation of the plant hormone auxin and the polar localization of the efflux protein PIN-FORMED1 (PIN1). The transcription factor MONOPTEROS (MP) plays a crucial role in orienting PIN1 polarity, thereby facilitating auxin-driven organogenesis. In this study, we investigate genes downstream of MP that may regulate PIN1 polarity and organogenesis, discovering that the downstream vascular transcription factor TMO5 can promote PIN1 polarity convergence non-cell-autonomously and that TMO5 and its family members promote organ initiation in the SAM. By examining the role of auxin and cytokinin downstream of these genes, we provide evidence that the TMO5-like genes control PIN1 polarity and drive organogenesis by coordinating multiple hormonal signalling pathways.

@article{kareem_water_2025,
	title = {Water availability positions auxin response maxima to determine plant regeneration fates},
	volume = {11},
	copyright = {2025 The Author(s)},
	issn = {2055-0278},
	url = {https://www.nature.com/articles/s41477-025-02029-2},
	doi = {10.1038/s41477-025-02029-2},
	abstract = {Wounding and hormones serve as diverse triggers for regeneration in animals and plants. Despite important advances in understanding various types of regeneration, the mechanism by which plants determine regeneration outcomes remains largely unknown. Here we demonstrate in Arabidopsis that a trade-off between two regeneration fates, wound-induced callus and root regeneration, was driven by distinct molecular pathways related to cambium and root development, respectively. We discovered that local water availability near the wound site determined the early stages of regeneration fates in Arabidopsis and tomato, with high water triggering root fate and low water initiating callus fate. Distinct spatial distributions of auxin response maxima around the wound, shaped by water availability, were critical for determining root or callus fates. We found that, by perturbing auxin response or auxin transport dynamics, we could change regeneration outcomes. Moreover, high water availability enhanced ethylene and jasmonic acid responses, whereas treatments with these hormones could modify auxin transport dynamics or the location of auxin response maxima, thus influencing regeneration fates. We propose that, through stress hormones, water availability modifies the auxin response distribution to control regeneration outcomes, thus allowing environmental control of regeneration and providing a means to improve in vitro regeneration by changing the water potential.},
	language = {en},
	number = {7},
	urldate = {2026-09-07},
	journal = {Nature Plants},
	publisher = {Nature Publishing Group},
	author = {Kareem, Abdul and van Wüllen, Anna K. and Zhang, Ai and Walckiers, Gabriel and Fasth, Ellen and Melnyk, Charles W.},
	month = jul,
	year = {2025},
	keywords = {Cell fate, Plant regeneration},
	pages = {1367--1379},
}

Wounding and hormones serve as diverse triggers for regeneration in animals and plants. Despite important advances in understanding various types of regeneration, the mechanism by which plants determine regeneration outcomes remains largely unknown. Here we demonstrate in Arabidopsis that a trade-off between two regeneration fates, wound-induced callus and root regeneration, was driven by distinct molecular pathways related to cambium and root development, respectively. We discovered that local water availability near the wound site determined the early stages of regeneration fates in Arabidopsis and tomato, with high water triggering root fate and low water initiating callus fate. Distinct spatial distributions of auxin response maxima around the wound, shaped by water availability, were critical for determining root or callus fates. We found that, by perturbing auxin response or auxin transport dynamics, we could change regeneration outcomes. Moreover, high water availability enhanced ethylene and jasmonic acid responses, whereas treatments with these hormones could modify auxin transport dynamics or the location of auxin response maxima, thus influencing regeneration fates. We propose that, through stress hormones, water availability modifies the auxin response distribution to control regeneration outcomes, thus allowing environmental control of regeneration and providing a means to improve in vitro regeneration by changing the water potential.

@article{serivichyaswat_auxin_2024,
	title = {Auxin signaling in the cambium promotes tissue adhesion and vascular formation during {Arabidopsis} graft healing},
	volume = {196},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiae257},
	doi = {10.1093/plphys/kiae257},
	abstract = {The strong ability of plants to regenerate wounds is exemplified by grafting when two plants are cut and joined together to grow as one. During graft healing, tissues attach, cells proliferate, and the vasculatures connect to form a graft union. The plant hormone auxin plays a central role, and auxin-related mutants perturb grafting success. Here, we investigated the role of individual cell types and their response to auxin during Arabidopsis (Arabidopsis thaliana) graft formation. By employing a cell-specific inducible misexpression system, we blocked auxin response in individual cell types using the bodenlos mutation. We found that auxin signaling in procambial tissues was critical for successful tissue attachment and vascular differentiation. In addition, we found that auxin signaling was required for cell divisions of the procambial cells during graft formation. Loss of function mutants in cambial pathways also perturbed attachment and phloem reconnection. We propose that cambial and procambial tissues drive tissue attachment and vascular differentiation during successful grafting. Our study thus refines our knowledge of graft development and furthers our understanding of the regenerative role of the cambium.},
	number = {2},
	urldate = {2026-09-07},
	journal = {Plant Physiology},
	author = {Serivichyaswat, Phanu T and Kareem, Abdul and Feng, Ming and Melnyk, Charles W},
	month = oct,
	year = {2024},
	pages = {754--762},
}

The strong ability of plants to regenerate wounds is exemplified by grafting when two plants are cut and joined together to grow as one. During graft healing, tissues attach, cells proliferate, and the vasculatures connect to form a graft union. The plant hormone auxin plays a central role, and auxin-related mutants perturb grafting success. Here, we investigated the role of individual cell types and their response to auxin during Arabidopsis (Arabidopsis thaliana) graft formation. By employing a cell-specific inducible misexpression system, we blocked auxin response in individual cell types using the bodenlos mutation. We found that auxin signaling in procambial tissues was critical for successful tissue attachment and vascular differentiation. In addition, we found that auxin signaling was required for cell divisions of the procambial cells during graft formation. Loss of function mutants in cambial pathways also perturbed attachment and phloem reconnection. We propose that cambial and procambial tissues drive tissue attachment and vascular differentiation during successful grafting. Our study thus refines our knowledge of graft development and furthers our understanding of the regenerative role of the cambium.

@article{feng_plant_2024,
	series = {Focus {Issue} on “{Unique} {Aspects} of {Plant} {Sciences}”},
	title = {Plant grafting: {Molecular} mechanisms and applications},
	volume = {17},
	issn = {1674-2052},
	shorttitle = {Plant grafting},
	url = {https://www.sciencedirect.com/science/article/pii/S1674205223004008},
	doi = {10.1016/j.molp.2023.12.006},
	abstract = {People have grafted plants since antiquity for propagation, to increase yields, and to improve stress tolerance. This cutting and joining of tissues activates an incredible regenerative ability as different plants fuse and grow as one. For over a hundred years, people have studied the scientific basis for how plants graft. Today, new techniques and a deepening knowledge of the molecular basis for graft formation have allowed a range of previously ungraftable combinations to emerge. Here, we review recent developments in our understanding of graft formation, including the attachment and vascular formation steps. We analyze why plants graft and how biotic and abiotic factors influence successful grafting. We also discuss the ability and inability of plants to graft, and how grafting has transformed both horticulture and fundamental plant science. As our knowledge about plant grafting improves, new combinations and techniques will emerge to allow an expanded use of grafting for horticultural applications and to address fundamental research questions.},
	number = {1},
	urldate = {2026-09-07},
	journal = {Molecular Plant},
	author = {Feng, Ming and Augstein, Frauke and Kareem, Abdul and Melnyk, Charles W.},
	month = jan,
	year = {2024},
	keywords = {mobile molecules, plant grafting, regeneration, stress tolerance, tissue adhesion, vascular differentiation},
	pages = {75--91},
}

People have grafted plants since antiquity for propagation, to increase yields, and to improve stress tolerance. This cutting and joining of tissues activates an incredible regenerative ability as different plants fuse and grow as one. For over a hundred years, people have studied the scientific basis for how plants graft. Today, new techniques and a deepening knowledge of the molecular basis for graft formation have allowed a range of previously ungraftable combinations to emerge. Here, we review recent developments in our understanding of graft formation, including the attachment and vascular formation steps. We analyze why plants graft and how biotic and abiotic factors influence successful grafting. We also discuss the ability and inability of plants to graft, and how grafting has transformed both horticulture and fundamental plant science. As our knowledge about plant grafting improves, new combinations and techniques will emerge to allow an expanded use of grafting for horticultural applications and to address fundamental research questions.

@article{zhang_cell-wall_2022,
	title = {Cell-wall damage activates {DOF} transcription factors to promote wound healing and tissue regeneration in \textit{{Arabidopsis} thaliana}},
	volume = {32},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982222003396},
	doi = {10.1016/j.cub.2022.02.069},
	abstract = {Wound healing is a fundamental property of plants and animals that requires recognition of cellular damage to initiate regeneration. In plants, wounding activates a defense response via the production of jasmonic acid and a regeneration response via the hormone auxin and several ethylene response factor (ERF) and NAC domain-containing protein (ANAC) transcription factors. To better understand how plants recognize damage and initiate healing, we searched for factors upregulated during the horticulturally relevant process of plant grafting and found four related DNA binding with one finger (DOF) transcription factors, HIGH CAMBIAL ACTIVITY2 (HCA2), TARGET OF MONOPTEROS6 (TMO6), DOF2.1, and DOF6, whose expression rapidly activated at the Arabidopsis graft junction. Grafting or wounding a quadruple hca2, tmo6, dof2.1, dof6 mutant inhibited vascular and cell-wall-related gene expression. Furthermore, the quadruple dof mutant reduced callus formation, tissue attachment, vascular regeneration, and pectin methylesterification in response to wounding. We also found that activation of DOF gene expression after wounding required auxin, but hormone treatment alone was insufficient for their induction. However, modifying cell walls by enzymatic digestion of cellulose or pectin greatly enhanced TMO6 and HCA2 expression, whereas genetic modifications to the pectin or cellulose matrix using the PECTIN METHYLESTERASE INHIBITOR5 overexpression line or korrigan1 mutant altered TMO6 and HCA2 expression. Changes to the cellulose or pectin matrix were also sufficient to activate the wound-associated ERF115 and ANAC096 transcription factors, suggesting that cell-wall damage represents a common mechanism for wound perception and the promotion of tissue regeneration.},
	number = {9},
	urldate = {2026-09-07},
	journal = {Current Biology},
	author = {Zhang, Ai and Matsuoka, Keita and Kareem, Abdul and Robert, Madalen and Roszak, Pawel and Blob, Bernhard and Bisht, Anchal and De Veylder, Lieven and Voiniciuc, Cătălin and Asahina, Masashi and Melnyk, Charles W.},
	month = may,
	year = {2022},
	keywords = {DOF transcription factors, auxin, cell walls, cell-wall damage, grafting, regeneration, wound healing},
	pages = {1883--1894.e7},
}

Wound healing is a fundamental property of plants and animals that requires recognition of cellular damage to initiate regeneration. In plants, wounding activates a defense response via the production of jasmonic acid and a regeneration response via the hormone auxin and several ethylene response factor (ERF) and NAC domain-containing protein (ANAC) transcription factors. To better understand how plants recognize damage and initiate healing, we searched for factors upregulated during the horticulturally relevant process of plant grafting and found four related DNA binding with one finger (DOF) transcription factors, HIGH CAMBIAL ACTIVITY2 (HCA2), TARGET OF MONOPTEROS6 (TMO6), DOF2.1, and DOF6, whose expression rapidly activated at the Arabidopsis graft junction. Grafting or wounding a quadruple hca2, tmo6, dof2.1, dof6 mutant inhibited vascular and cell-wall-related gene expression. Furthermore, the quadruple dof mutant reduced callus formation, tissue attachment, vascular regeneration, and pectin methylesterification in response to wounding. We also found that activation of DOF gene expression after wounding required auxin, but hormone treatment alone was insufficient for their induction. However, modifying cell walls by enzymatic digestion of cellulose or pectin greatly enhanced TMO6 and HCA2 expression, whereas genetic modifications to the pectin or cellulose matrix using the PECTIN METHYLESTERASE INHIBITOR5 overexpression line or korrigan1 mutant altered TMO6 and HCA2 expression. Changes to the cellulose or pectin matrix were also sufficient to activate the wound-associated ERF115 and ANAC096 transcription factors, suggesting that cell-wall damage represents a common mechanism for wound perception and the promotion of tissue regeneration.

@article{varapparambath_mechanical_2022,
	title = {Mechanical conflict caused by a cell-wall-loosening enzyme activates \textit{de novo} shoot regeneration},
	volume = {57},
	issn = {1534-5807},
	url = {https://www.sciencedirect.com/science/article/pii/S1534580722005482},
	doi = {10.1016/j.devcel.2022.07.017},
	abstract = {Cellular heterogeneity is a hallmark of multicellular organisms. During shoot regeneration from undifferentiated callus, only a select few cells, called progenitors, develop into shoot. How these cells are selected and what governs their subsequent progression to a patterned organ system is unknown. Using Arabidopsis thaliana, we show that it is not just the abundance of stem cell regulators but rather the localization pattern of polarity proteins that predicts the progenitor’s fate. A shoot-promoting factor, CUC2, activated the expression of the cell-wall-loosening enzyme, XTH9, solely in a shell of cells surrounding the progenitor, causing different mechanical stresses in these cells. This mechanical conflict then activates cell polarity in progenitors to promote meristem formation. Interestingly, genetic or physical perturbations to cells surrounding the progenitor impaired the progenitor and vice versa. These suggest a feedback loop between progenitors and their neighbors for shoot regeneration in the absence of tissue-patterning cues.},
	number = {17},
	urldate = {2026-09-07},
	journal = {Developmental Cell},
	author = {Varapparambath, Vijina and Mathew, Mabel Maria and Shanmukhan, Anju Pallipurath and Radhakrishnan, Dhanya and Kareem, Abdul and Verma, Shubham and Ramalho, João Jacob and Manoj, Bejoy and Vellandath, Archana Rajan and Aiyaz, Mohammed and Radha, Raji Krishna and Landge, Amit N. and Mähönen, Ari Pekka and Heisler, Marcus G. and Weijers, Dolf and Prasad, Kalika},
	month = sep,
	year = {2022},
	keywords = {CUC2, auxin, cell polarity, cell-wall-loosening enzyme, mechanical conflict, shoot regeneration},
	pages = {2063--2080.e10},
}

Cellular heterogeneity is a hallmark of multicellular organisms. During shoot regeneration from undifferentiated callus, only a select few cells, called progenitors, develop into shoot. How these cells are selected and what governs their subsequent progression to a patterned organ system is unknown. Using Arabidopsis thaliana, we show that it is not just the abundance of stem cell regulators but rather the localization pattern of polarity proteins that predicts the progenitor’s fate. A shoot-promoting factor, CUC2, activated the expression of the cell-wall-loosening enzyme, XTH9, solely in a shell of cells surrounding the progenitor, causing different mechanical stresses in these cells. This mechanical conflict then activates cell polarity in progenitors to promote meristem formation. Interestingly, genetic or physical perturbations to cells surrounding the progenitor impaired the progenitor and vice versa. These suggest a feedback loop between progenitors and their neighbors for shoot regeneration in the absence of tissue-patterning cues.

@article{kareem_pin-formed1_2022,
	title = {{PIN}-{FORMED1} polarity in the plant shoot epidermis is insensitive to the polarity of neighboring cells},
	volume = {25},
	issn = {2589-0042},
	url = {https://www.sciencedirect.com/science/article/pii/S2589004222013347},
	doi = {10.1016/j.isci.2022.105062},
	abstract = {At the Arabidopsis shoot apex, epidermal cells are planar-polarized along an axis marked by the asymmetric localization patterns of several proteins including PIN-FORMED1 (PIN1), which facilitates the directional efflux of the plant hormone auxin to pattern phyllotaxis. While PIN1 polarity is known to be regulated non-cell autonomously via the MONOPTEROS (MP) transcription factor, how this occurs has not been determined. Here, we use mosaic expression of the serine threonine kinase PINOID (PID) to test whether PIN1 polarizes according to the polarity of neighboring cells. Our findings reveal that PIN1 is insensitive to the polarity of PIN1 in neighboring cells arguing against auxin flux or extracellular auxin concentrations acting as a polarity cue, in contrast to previous model proposals.},
	number = {10},
	urldate = {2026-09-07},
	journal = {iScience},
	author = {Kareem, Abdul and Bhatia, Neha and Ohno, Carolyn and Heisler, Marcus G.},
	month = oct,
	year = {2022},
	keywords = {Biological sciences, Plant biology, Plant development, Plant morphology},
	pages = {105062},
}

At the Arabidopsis shoot apex, epidermal cells are planar-polarized along an axis marked by the asymmetric localization patterns of several proteins including PIN-FORMED1 (PIN1), which facilitates the directional efflux of the plant hormone auxin to pattern phyllotaxis. While PIN1 polarity is known to be regulated non-cell autonomously via the MONOPTEROS (MP) transcription factor, how this occurs has not been determined. Here, we use mosaic expression of the serine threonine kinase PINOID (PID) to test whether PIN1 polarizes according to the polarity of neighboring cells. Our findings reveal that PIN1 is insensitive to the polarity of PIN1 in neighboring cells arguing against auxin flux or extracellular auxin concentrations acting as a polarity cue, in contrast to previous model proposals.

@article{radhakrishnan_age_2021,
	title = {Age, {Wound} {Size} and {Position} of {Injury} – {Dependent} {Vascular} {Regeneration} {Assay} in {Growing} {Leaves}},
	volume = {11},
	url = {https://bio-protocol.org/en/bpdetail?id=4010&type=0},
	doi = {10.21769/BioProtoc.4010},
	abstract = {Recurring damage to the aerial organs of plants necessitates their prompt repair, particularly their vasculature. While vascular regeneration assays for aerial plant parts such as the stem and inflorescence stalk are well established, those for leaf vasculature remain unexplored. Recently, we established a new vascular regeneration assay in growing leaves and discovered the underlying molecular mechanism. Here, we describe the detailed stepwise method for the incision and regeneration assay used to study leaf vascular regeneration. By using a combination of micro-surgical perturbations, brightfield microscopy, and other experimental approaches, we further show that the age of the leaf as well as the position and size of the injury determine the overall success rate of regeneration. This easy-to-master vascular regeneration assay is an efficient and rapid method to study the mechanism of vascular regeneration in growing leaves. The assay can be readily combined with cellular and molecular biology techniques.},
	language = {en},
	number = {9},
	urldate = {2026-09-07},
	journal = {Bio-protocol},
	author = {Radhakrishnan, Dhanya and Shanmukhan, Anju Pallipurath and Kareem, Abdul and Mathew, Mabel Maria and Varaparambathu, Vijina and Aiyaz, Mohammed and Radha, Raji Krishna and Mekala, Krishnaprashanth Ramesh and Shaji, Anil and Prasad, Kalika},
	month = may,
	year = {2021},
}

Recurring damage to the aerial organs of plants necessitates their prompt repair, particularly their vasculature. While vascular regeneration assays for aerial plant parts such as the stem and inflorescence stalk are well established, those for leaf vasculature remain unexplored. Recently, we established a new vascular regeneration assay in growing leaves and discovered the underlying molecular mechanism. Here, we describe the detailed stepwise method for the incision and regeneration assay used to study leaf vascular regeneration. By using a combination of micro-surgical perturbations, brightfield microscopy, and other experimental approaches, we further show that the age of the leaf as well as the position and size of the injury determine the overall success rate of regeneration. This easy-to-master vascular regeneration assay is an efficient and rapid method to study the mechanism of vascular regeneration in growing leaves. The assay can be readily combined with cellular and molecular biology techniques.

@article{shanmukhan_regulation_2021,
	title = {Regulation of touch-stimulated de novo root regeneration from {Arabidopsis} leaves},
	volume = {187},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiab286},
	doi = {10.1093/plphys/kiab286},
	abstract = {Dear Editor,Among several of the plant’s lateral organs, leaves show versatile regenerative responses, be it natural, mechanical-injury induced, or tissue culture-mediated. Regeneration of entire plants from various species of Kalanchoe leaves is an example of natural regeneration from leaf (Smith et al., 2019). In tissue culture-mediated regeneration, small leaf explants can give rise to entire shoot and/root system via callus in the presence of hormonal supplements. The incised mid-vein of an undetached growing leaf, and the cut end of detached leaves exhibit regenerative responses, both of which fall under mechanical injury-induced regeneration. Although mid-vein regeneration in growing leaves was investigated only recently, mechanical injury-induced regenerative responses at the cut end of detached leaves have been studied for several years (Chen et al., 2014; Ikeuchi et al., 2016; Bustillo-Avendaño et al., 2018; Zhang et al., 2019; Radhakrishnan et al., 2020). Studies in Arabidopsis (Arabidopsis thaliana) reported the emergence of adventitious roots from the cut end of detached leaves, be it the base of leaf blade or the petiole via de novo root regeneration (DNRR; Chen et al., 2014; Bustillo-Avendaño et al., 2018). This ability of part of a tissue to produce an organ, whose identity is different from its parent tissue, is rather intriguing. However, DNRR is not the only response observed at the cut end of a detached Arabidopsis leaf; wound healing in the form of callus formation occurs at the cut end of leaves that do not undergo DNRR. With the available data, it was unclear if the decision to make callus or DNRR is random or if any external inductive cues favor one over the other. It was therefore imperative to investigate this differential regenerative response to the same injury in the same organ. Using various experimental approaches, we show that the factor favoring DNRR over callus formation is the direct physical contact of the cut end to any solid or liquid surface. Interestingly, the plant hormone auxin shows elevated accumulation in response to touch to the wound site. We further show that PLETHORA (PLT) genes, which are essential as well as sufficient for DNRR, regulate this process via a mechanism distinct from PLT-regulated lateral root (LR) formation or other PLT-regulated regenerative responses.},
	number = {1},
	urldate = {2026-09-07},
	journal = {Plant Physiology},
	author = {Shanmukhan, Anju Pallipurath and Mathew, Mabel Maria and Aiyaz, Mohammed and Varaparambathu, Vijina and Kareem, Abdul and Radhakrishnan, Dhanya and Prasad, Kalika},
	month = sep,
	year = {2021},
	pages = {52--58},
}

Dear Editor,Among several of the plant’s lateral organs, leaves show versatile regenerative responses, be it natural, mechanical-injury induced, or tissue culture-mediated. Regeneration of entire plants from various species of Kalanchoe leaves is an example of natural regeneration from leaf (Smith et al., 2019). In tissue culture-mediated regeneration, small leaf explants can give rise to entire shoot and/root system via callus in the presence of hormonal supplements. The incised mid-vein of an undetached growing leaf, and the cut end of detached leaves exhibit regenerative responses, both of which fall under mechanical injury-induced regeneration. Although mid-vein regeneration in growing leaves was investigated only recently, mechanical injury-induced regenerative responses at the cut end of detached leaves have been studied for several years (Chen et al., 2014; Ikeuchi et al., 2016; Bustillo-Avendaño et al., 2018; Zhang et al., 2019; Radhakrishnan et al., 2020). Studies in Arabidopsis (Arabidopsis thaliana) reported the emergence of adventitious roots from the cut end of detached leaves, be it the base of leaf blade or the petiole via de novo root regeneration (DNRR; Chen et al., 2014; Bustillo-Avendaño et al., 2018). This ability of part of a tissue to produce an organ, whose identity is different from its parent tissue, is rather intriguing. However, DNRR is not the only response observed at the cut end of a detached Arabidopsis leaf; wound healing in the form of callus formation occurs at the cut end of leaves that do not undergo DNRR. With the available data, it was unclear if the decision to make callus or DNRR is random or if any external inductive cues favor one over the other. It was therefore imperative to investigate this differential regenerative response to the same injury in the same organ. Using various experimental approaches, we show that the factor favoring DNRR over callus formation is the direct physical contact of the cut end to any solid or liquid surface. Interestingly, the plant hormone auxin shows elevated accumulation in response to touch to the wound site. We further show that PLETHORA (PLT) genes, which are essential as well as sufficient for DNRR, regulate this process via a mechanism distinct from PLT-regulated lateral root (LR) formation or other PLT-regulated regenerative responses.

@article{radhakrishnan_coherent_2020,
	title = {A coherent feed-forward loop drives vascular regeneration in damaged aerial organs of plants growing in a normal developmental context},
	volume = {147},
	issn = {0950-1991},
	url = {https://doi.org/10.1242/dev.185710},
	doi = {10.1242/dev.185710},
	abstract = {Aerial organs of plants, being highly prone to local injuries, require tissue restoration to ensure their survival. However, knowledge of the underlying mechanism is sparse. In this study, we mimicked natural injuries in growing leaves and stems to study the reunion between mechanically disconnected tissues. We show that PLETHORA (PLT) and AINTEGUMENTA (ANT) genes, which encode stem cell-promoting factors, are activated and contribute to vascular regeneration in response to these injuries. PLT proteins bind to and activate the CUC2 promoter. PLT proteins and CUC2 regulate the transcription of the local auxin biosynthesis gene YUC4 in a coherent feed-forward loop, and this process is necessary to drive vascular regeneration. In the absence of this PLT-mediated regeneration response, leaf ground tissue cells can neither acquire the early vascular identity marker ATHB8, nor properly polarise auxin transporters to specify new venation paths. The PLT-CUC2 module is required for vascular regeneration, but is dispensable for midvein formation in leaves. We reveal the mechanisms of vascular regeneration in plants and distinguish between the wound-repair ability of the tissue and its formation during normal development.},
	number = {6},
	urldate = {2026-09-07},
	journal = {Development},
	author = {Radhakrishnan, Dhanya and Shanmukhan, Anju Pallipurath and Kareem, Abdul and Aiyaz, Mohammed and Varapparambathu, Vijina and Toms, Ashna and Kerstens, Merijn and Valsakumar, Devisree and Landge, Amit N. and Shaji, Anil and Mathew, Mathew K. and Sawchuk, Megan G. and Scarpella, Enrico and Krizek, Beth A. and Efroni, Idan and Mähönen, Ari Pekka and Willemsen, Viola and Scheres, Ben and Prasad, Kalika},
	month = mar,
	year = {2020},
	pages = {dev185710},
}

Aerial organs of plants, being highly prone to local injuries, require tissue restoration to ensure their survival. However, knowledge of the underlying mechanism is sparse. In this study, we mimicked natural injuries in growing leaves and stems to study the reunion between mechanically disconnected tissues. We show that PLETHORA (PLT) and AINTEGUMENTA (ANT) genes, which encode stem cell-promoting factors, are activated and contribute to vascular regeneration in response to these injuries. PLT proteins bind to and activate the CUC2 promoter. PLT proteins and CUC2 regulate the transcription of the local auxin biosynthesis gene YUC4 in a coherent feed-forward loop, and this process is necessary to drive vascular regeneration. In the absence of this PLT-mediated regeneration response, leaf ground tissue cells can neither acquire the early vascular identity marker ATHB8, nor properly polarise auxin transporters to specify new venation paths. The PLT-CUC2 module is required for vascular regeneration, but is dispensable for midvein formation in leaves. We reveal the mechanisms of vascular regeneration in plants and distinguish between the wound-repair ability of the tissue and its formation during normal development.

@article{nishad_modulation_2020,
	title = {Modulation of {Plant} {Defense} {System} in {Response} to {Microbial} {Interactions}},
	volume = {11},
	issn = {1664-302X},
	url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2020.01298/full},
	doi = {10.3389/fmicb.2020.01298},
	abstract = {At different stages throughout their life cycle, plants often encounter several pathogenic microbes that challenge plant growth and development. The sophisticated plant innate immune system prevents the growth of harmful microbes via two interconnected defense strategies based on pathogen perception. These strategies involve microbe-associated molecular pattern-triggered immunity and microbial effector-triggered immunity. Both these immune responses induce several defense mechanisms for restricting pathogen attack to protect against pathogens and terminate their growth. Plants often develop immune memory after an exposure to pathogens, leading to systemic acquired resistance. Unlike that with harmful microbes, plants make friendly interactions with beneficial microbes for boosting their plant immune system. A spike in recent publications has further improved our understanding of the immune responses in plants as triggered by interactions with microbes. The present study reviews our current understanding of how plant–microbe interactions can activate the sophisticated plant immune system at the molecular level. We further discuss, how plant-microbe interaction boost the immune system of plants by demonstrating the examples of Mycorrhizal and Rhizobial association and how these plant-microbe interactions can be exploited to engineer disease resistance and crop improvement.},
	language = {English},
	urldate = {2026-09-07},
	journal = {Frontiers in Microbiology},
	publisher = {Frontiers},
	author = {Nishad, Resna and Ahmed, Talaat and Rahman, Vattakandy Jasin and Kareem, Abdul},
	month = jul,
	year = {2020},
	keywords = {Effector- triggered immunity, MAMP-triggered immunity, Mycorrhiza-induced resistance, Plant Immunity, beneficial microbes, innate immunity},
}

At different stages throughout their life cycle, plants often encounter several pathogenic microbes that challenge plant growth and development. The sophisticated plant innate immune system prevents the growth of harmful microbes via two interconnected defense strategies based on pathogen perception. These strategies involve microbe-associated molecular pattern-triggered immunity and microbial effector-triggered immunity. Both these immune responses induce several defense mechanisms for restricting pathogen attack to protect against pathogens and terminate their growth. Plants often develop immune memory after an exposure to pathogens, leading to systemic acquired resistance. Unlike that with harmful microbes, plants make friendly interactions with beneficial microbes for boosting their plant immune system. A spike in recent publications has further improved our understanding of the immune responses in plants as triggered by interactions with microbes. The present study reviews our current understanding of how plant–microbe interactions can activate the sophisticated plant immune system at the molecular level. We further discuss, how plant-microbe interaction boost the immune system of plants by demonstrating the examples of Mycorrhizal and Rhizobial association and how these plant-microbe interactions can be exploited to engineer disease resistance and crop improvement.

@article{durgaprasad_gradient_2019,
	title = {Gradient {Expression} of {Transcription} {Factor} {Imposes} a {Boundary} on {Organ} {Regeneration} {Potential} in {Plants}},
	volume = {29},
	issn = {2211-1247},
	url = {https://www.sciencedirect.com/science/article/pii/S2211124719311611},
	doi = {10.1016/j.celrep.2019.08.099},
	abstract = {A wide variety of multicellular organisms across the kingdoms display remarkable ability to restore their tissues or organs when they suffer damage. However, the ability to repair damage is not uniformly distributed throughout body parts. Here, we unravel the elusive mechanistic basis of boundaries on organ regeneration potential using root tip resection as a model and show that the dosage of gradient-expressed PLT2 transcription factor is the underlying cause. While transient downregulation of PLT2 in distinct set of plt mutant backgrounds renders meristematic cells incapable of regeneration, forced expression of PLT2 acts through auto-activation to confer regeneration potential to the cells undergoing differentiation. Surprisingly, sustained exposure to nuclear PLT2, beyond a threshold, leads to reduction of regeneration potential despite giving rise to longer meristem. Our studies reveal dosage-dependent role of gradient-expressed PLT2 in root tip regeneration and uncouple the size of an organ from its regeneration potential.},
	number = {2},
	urldate = {2026-09-07},
	journal = {Cell Reports},
	author = {Durgaprasad, Kavya and Roy, Merin V. and Venugopal M., Anjali and Kareem, Abdul and Raj, Kiran and Willemsen, Viola and Mähönen, Ari Pekka and Scheres, Ben and Prasad, Kalika},
	month = oct,
	year = {2019},
	keywords = {PLETHORA gradient, autoregulation, dosage dependent, lateral root, multicellular organism, organ regeneration, organ size, root meristem, stem cells},
	pages = {453--463.e3},
}

A wide variety of multicellular organisms across the kingdoms display remarkable ability to restore their tissues or organs when they suffer damage. However, the ability to repair damage is not uniformly distributed throughout body parts. Here, we unravel the elusive mechanistic basis of boundaries on organ regeneration potential using root tip resection as a model and show that the dosage of gradient-expressed PLT2 transcription factor is the underlying cause. While transient downregulation of PLT2 in distinct set of plt mutant backgrounds renders meristematic cells incapable of regeneration, forced expression of PLT2 acts through auto-activation to confer regeneration potential to the cells undergoing differentiation. Surprisingly, sustained exposure to nuclear PLT2, beyond a threshold, leads to reduction of regeneration potential despite giving rise to longer meristem. Our studies reveal dosage-dependent role of gradient-expressed PLT2 in root tip regeneration and uncouple the size of an organ from its regeneration potential.

@article{landge_intermediate_2018,
	title = {Intermediate {Developmental} {Phases} {During} {Regeneration}},
	volume = {59},
	issn = {0032-0781},
	url = {https://doi.org/10.1093/pcp/pcy011},
	doi = {10.1093/pcp/pcy011},
	abstract = {The initial view that regeneration can be a continuum in terms of regulatory mechanisms is gradually changing, and recent evidence points towards the presence of discrete regulatory steps and intermediate phases. Furthermore, regeneration presents an excellent example of a process generating order and pattern, i.e. a self-organization process. It is likely that the process traverses a set of intermediate phases before reaching an endpoint. Although some progress has been made in deciphering the identity of these intermediate phases, a lot more work is needed to derive a comprehensive and complete picture. Here, we discuss the intermediate developmental phases in plant regeneration and compare them with the possible intermediate developmental phases in animal regeneration.},
	number = {4},
	urldate = {2026-09-07},
	journal = {Plant and Cell Physiology},
	author = {Landge, Amit N and Radhakrishnan, Dhanya and Kareem, Abdul and Prasad, Kalika},
	month = apr,
	year = {2018},
	pages = {707--712},
}

The initial view that regeneration can be a continuum in terms of regulatory mechanisms is gradually changing, and recent evidence points towards the presence of discrete regulatory steps and intermediate phases. Furthermore, regeneration presents an excellent example of a process generating order and pattern, i.e. a self-organization process. It is likely that the process traverses a set of intermediate phases before reaching an endpoint. Although some progress has been made in deciphering the identity of these intermediate phases, a lot more work is needed to derive a comprehensive and complete picture. Here, we discuss the intermediate developmental phases in plant regeneration and compare them with the possible intermediate developmental phases in animal regeneration.

@article{radhakrishnan_shoot_2018,
	series = {Growth and development},
	title = {Shoot regeneration: a journey from acquisition of competence to completion},
	volume = {41},
	issn = {1369-5266},
	shorttitle = {Shoot regeneration},
	url = {https://www.sciencedirect.com/science/article/pii/S136952661730095X},
	doi = {10.1016/j.pbi.2017.08.001},
	abstract = {Plants display an extraordinary ability to regenerate complete shoot systems from a tissue fragment or even from a single cell. Upregulation of the determinants of pluripotency during a precise window of time in response to external inductive cues is a key decisive factor for shoot regeneration. A burst of recent studies has begun to provide an understanding of signaling molecules that are instrumental in the making of the regenerative mass, as well as the developmental regulators that are seminal in shaping the pluripotent state. Here, we discuss how signaling molecules, waves of mutually exclusive stem cell regulators and epigenetic modifiers could contribute to cellular heterogeneity in an island of regenerative mass, thus leading to de novo shoot regeneration.},
	urldate = {2026-09-07},
	journal = {Current Opinion in Plant Biology},
	author = {Radhakrishnan, Dhanya and Kareem, Abdul and Durgaprasad, Kavya and Sreeraj, E and Sugimoto, Kaoru and Prasad, Kalika},
	month = feb,
	year = {2018},
	pages = {23--31},
}

Plants display an extraordinary ability to regenerate complete shoot systems from a tissue fragment or even from a single cell. Upregulation of the determinants of pluripotency during a precise window of time in response to external inductive cues is a key decisive factor for shoot regeneration. A burst of recent studies has begun to provide an understanding of signaling molecules that are instrumental in the making of the regenerative mass, as well as the developmental regulators that are seminal in shaping the pluripotent state. Here, we discuss how signaling molecules, waves of mutually exclusive stem cell regulators and epigenetic modifiers could contribute to cellular heterogeneity in an island of regenerative mass, thus leading to de novo shoot regeneration.

@article{rajasekharan_genetic_2017,
	title = {Genetic diversity in {Oroxylum} indicum ({L}.) {Vent}., a threatened medicinal plants from {India} by {ISSR} analysis},
	copyright = {{\textless}img src='http://nopr.niscair.res.in/image/cc-license-sml.png'{\textgreater} {\textless}a href='http://creativecommons.org/licenses/by-nc-nd/2.5/in' target='\_blank'{\textgreater}CC Attribution-Noncommercial-No Derivative Works 2.5 India{\textless}/a{\textgreater}},
	issn = {0975-0967 (Online); 0972-5849 (Print)},
	url = {http://nopr.niscpr.res.in/handle/123456789/43335},
	abstract = {{\textless}em{\textgreater}Oroxylum indicum{\textless}/em{\textgreater} is an important threatened traditional medicinal plant native to Indian subcontinent. Inter Simple Sequence Repeats (ISSR) markers were used to assess the genetic diversity and population genetic structure of 39 accessions of {\textless}em{\textgreater}O. indicum {\textless}/em{\textgreater} belonging to South and North East India. A total of 92 discernible bands were generated from 17 primers, with 81 (88.04\%) being polymorphic, indicating high genetic diversity at the species level. The Nei’s gene diversity ({\textless}em{\textgreater}h{\textless}/em{\textgreater}) was estimated to be 0.2526 within populations, and 0.4027 at the species level. Analysis of molecular variance (AMOVA) showed that the genetic variation was found mainly among populations (68\%), but variance within populations was only 32\%. In addition, Nei’s differentiation coefficients ({\textless}em{\textgreater}G{\textless}/em{\textgreater}$_{\textrm{ST}}$) was found to be high (0.3733), confirming the relatively high level of genetic differentiation among populations. The unweighted pair group method of arithmetic-average (UPGMA) clustering also demonstrated high genetic differentiation between South and North East Indian populations. The estimated gene flow ({\textless}em{\textgreater}N{\textless}/em{\textgreater}m) from {\textless}em{\textgreater}G{\textless}/em{\textgreater}$_{\textrm{ST}}$ was 0.8393. It indicated that the fragmentation of populations and anthropogenic activities might result in specific evolutionary history. Based on the genetic data, a conservation strategy is proposed for this threatened species.},
	language = {en\_US},
	urldate = {2026-09-07},
	journal = {IJBT Vol.16(3) [July 2017]},
	publisher = {NISCAIR-CSIR, India},
	author = {Rajasekharan, P. E. and Kareem, V. K. Abdul and Ravish, B. S. and Mini, S.},
	month = jul,
	year = {2017},
	note = {Accepted: 2018-01-04T06:22:34Z},
}

\textlessem\textgreaterOroxylum indicum\textless/em\textgreater is an important threatened traditional medicinal plant native to Indian subcontinent. Inter Simple Sequence Repeats (ISSR) markers were used to assess the genetic diversity and population genetic structure of 39 accessions of \textlessem\textgreaterO. indicum \textless/em\textgreater belonging to South and North East India. A total of 92 discernible bands were generated from 17 primers, with 81 (88.04%) being polymorphic, indicating high genetic diversity at the species level. The Nei’s gene diversity (\textlessem\textgreaterh\textless/em\textgreater) was estimated to be 0.2526 within populations, and 0.4027 at the species level. Analysis of molecular variance (AMOVA) showed that the genetic variation was found mainly among populations (68%), but variance within populations was only 32%. In addition, Nei’s differentiation coefficients (\textlessem\textgreaterG\textless/em\textgreater$_{\textrm{ST}}$) was found to be high (0.3733), confirming the relatively high level of genetic differentiation among populations. The unweighted pair group method of arithmetic-average (UPGMA) clustering also demonstrated high genetic differentiation between South and North East Indian populations. The estimated gene flow (\textlessem\textgreaterN\textless/em\textgreaterm) from \textlessem\textgreaterG\textless/em\textgreater$_{\textrm{ST}}$ was 0.8393. It indicated that the fragmentation of populations and anthropogenic activities might result in specific evolutionary history. Based on the genetic data, a conservation strategy is proposed for this threatened species.

@article{rajasekharan_issr_2017,
	title = {{ISSR} analysis reveals low genetic diversity and high genetic differentiation in {Kaempferia} galanga {L}. in {South} {India} populations},
	copyright = {{\textless}img src='http://nopr.niscair.res.in/image/cc-license-sml.png'{\textgreater} {\textless}a href='http://creativecommons.org/licenses/by-nc-nd/2.5/in' target='\_blank'{\textgreater}CC Attribution-Noncommercial-No Derivative Works 2.5 India{\textless}/a{\textgreater}},
	issn = {0975-0967 (Online); 0972-5849 (Print)},
	url = {http://nopr.niscpr.res.in/handle/123456789/43337},
	abstract = {{\textless}em{\textgreater}Kaempferia galanga  {\textless}/em{\textgreater} is an important medicinal herb used in many ayurvedic drug preparations.We investigated the genetic diversity and structure of 4 populations of {\textless}em{\textgreater}K. galanga{\textless}/em{\textgreater} collected from South India using inter simple sequence repeat (ISSR) markers. A low level genetic diversity was noticed among the populations (PPB= 44.45\%; {\textless}em{\textgreater}h{\textless}/em{\textgreater}= 0.1517 and {\textless}em{\textgreater}I{\textless}/em{\textgreater} = 0.2309). Average diversity within population was also low (PPB= 23.29\%; {\textless}em{\textgreater}h{\textless}/em{\textgreater} = 0.1003; {\textless}em{\textgreater}I{\textless}/em{\textgreater} = 0.1439) and the highest genetic diversity was observed in Shimoga population (PPB= 27.27\%; {\textless}em{\textgreater}h{\textless}/em{\textgreater} = 0.112; {\textless}em{\textgreater}I{\textless}/em{\textgreater} = 0.1625). Nei’s differentiation coefficients ({\textless}em{\textgreater}G{\textless}/em{\textgreater}$_{\textrm{ST}}$) was found to be high (0.3942) and the gene flow ({\textless}em{\textgreater}N{\textless}/em{\textgreater}m) was low (0.7683), confirming the high population genetic differentiation. The unweighted pair-group method using arithmetic average (UPGMA) clustering demonstrated similar results. Based on the overall low genetic diversity and high genetic differentiation among {\textless}em{\textgreater}K. galanga{\textless}/em{\textgreater} populations in South India, a conservation strategy is proposed.},
	language = {en\_US},
	urldate = {2026-09-07},
	journal = {IJBT Vol.16(3) [July 2017]},
	publisher = {NISCAIR-CSIR, India},
	author = {Rajasekharan, P. E. and Kareem, V. K. Abdul and Ravish, B. S. and Mini, S.},
	month = jul,
	year = {2017},
	note = {Accepted: 2018-01-04T07:13:16Z},
}

\textlessem\textgreaterKaempferia galanga  \textless/em\textgreater is an important medicinal herb used in many ayurvedic drug preparations.We investigated the genetic diversity and structure of 4 populations of \textlessem\textgreaterK. galanga\textless/em\textgreater collected from South India using inter simple sequence repeat (ISSR) markers. A low level genetic diversity was noticed among the populations (PPB= 44.45%; \textlessem\textgreaterh\textless/em\textgreater= 0.1517 and \textlessem\textgreaterI\textless/em\textgreater = 0.2309). Average diversity within population was also low (PPB= 23.29%; \textlessem\textgreaterh\textless/em\textgreater = 0.1003; \textlessem\textgreaterI\textless/em\textgreater = 0.1439) and the highest genetic diversity was observed in Shimoga population (PPB= 27.27%; \textlessem\textgreaterh\textless/em\textgreater = 0.112; \textlessem\textgreaterI\textless/em\textgreater = 0.1625). Nei’s differentiation coefficients (\textlessem\textgreaterG\textless/em\textgreater$_{\textrm{ST}}$) was found to be high (0.3942) and the gene flow (\textlessem\textgreaterN\textless/em\textgreaterm) was low (0.7683), confirming the high population genetic differentiation. The unweighted pair-group method using arithmetic average (UPGMA) clustering demonstrated similar results. Based on the overall low genetic diversity and high genetic differentiation among \textlessem\textgreaterK. galanga\textless/em\textgreater populations in South India, a conservation strategy is proposed.

@article{kareem_novo_2016,
	title = {De novo assembly of plant body plan: a step ahead of {Deadpool}},
	volume = {3},
	copyright = {© 2016 The Authors. Regeneration published by John Wiley \& Sons Ltd.},
	issn = {2052-4412},
	shorttitle = {De novo assembly of plant body plan},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/reg2.68},
	doi = {10.1002/reg2.68},
	abstract = {While in the movie Deadpool it is possible for a human to recreate an arm from scratch, in reality plants can even surpass that. Not only can they regenerate lost parts, but also the whole plant body can be reborn from a few existing cells. Despite the decades old realization that plant cells possess the ability to regenerate a complete shoot and root system, it is only now that the underlying mechanisms are being unraveled. De novo plant regeneration involves the initiation of regenerative mass, acquisition of the pluripotent state, reconstitution of stem cells and assembly of regulatory interactions. Recent studies have furthered our understanding on the making of a complete plant system in the absence of embryonic positional cues. We review the recent studies probing the molecular mechanisms of de novo plant regeneration in response to external inductive cues and our current knowledge of direct reprogramming of root to shoot and vice versa. We further discuss how de novo regeneration can be exploited to meet the demands of green culture industries and to serve as a general model to address the fundamental questions of regeneration across the plant kingdom.},
	language = {en},
	number = {4},
	urldate = {2026-09-07},
	journal = {Regeneration},
	author = {Kareem, Abdul and Radhakrishnan, Dhanya and Sondhi, Yash and Aiyaz, Mohammed and Roy, Merin V. and Sugimoto, Kaoru and Prasad, Kalika},
	year = {2016},
	keywords = {auxin, callus, cytokinin, de novo organogenesis, pluripotency, regeneration, stem cells, transdifferentiation},
	pages = {182--197},
}

While in the movie Deadpool it is possible for a human to recreate an arm from scratch, in reality plants can even surpass that. Not only can they regenerate lost parts, but also the whole plant body can be reborn from a few existing cells. Despite the decades old realization that plant cells possess the ability to regenerate a complete shoot and root system, it is only now that the underlying mechanisms are being unraveled. De novo plant regeneration involves the initiation of regenerative mass, acquisition of the pluripotent state, reconstitution of stem cells and assembly of regulatory interactions. Recent studies have furthered our understanding on the making of a complete plant system in the absence of embryonic positional cues. We review the recent studies probing the molecular mechanisms of de novo plant regeneration in response to external inductive cues and our current knowledge of direct reprogramming of root to shoot and vice versa. We further discuss how de novo regeneration can be exploited to meet the demands of green culture industries and to serve as a general model to address the fundamental questions of regeneration across the plant kingdom.

@article{kareem_protocol_2016,
	title = {Protocol: a method to study the direct reprogramming of lateral root primordia to fertile shoots},
	volume = {12},
	issn = {1746-4811},
	shorttitle = {Protocol},
	url = {https://doi.org/10.1186/s13007-016-0127-5},
	doi = {10.1186/s13007-016-0127-5},
	abstract = {Plants have the remarkable property to elaborate entire body plan from any tissue part. The conversion of lateral root primordium (LRP) to shoot is an ideal method for plant propagation and for plant researchers to understand the mechanism underlying trans-differentiation. Until now, however, a robust method that allows the efficient conversion of LRP to shoot is lacking. This has limited our ability to study the dynamic phases of reprogramming at cellular and molecular levels.},
	language = {en},
	number = {1},
	urldate = {2026-09-07},
	journal = {Plant Methods},
	author = {Kareem, Abdul and Radhakrishnan, Dhanya and Wang, Xin and Bagavathiappan, Subhikshaa and Trivedi, Zankhana B. and Sugimoto, Kaoru and Xu, Jian and Mähönen, Ari Pekka and Prasad, Kalika},
	month = may,
	year = {2016},
	keywords = {Arabidopsis, Auxin, Cytokinin, Lateral root, Regeneration, Shoot, Trans-differentiation},
	pages = {27},
}

Plants have the remarkable property to elaborate entire body plan from any tissue part. The conversion of lateral root primordium (LRP) to shoot is an ideal method for plant propagation and for plant researchers to understand the mechanism underlying trans-differentiation. Until now, however, a robust method that allows the efficient conversion of LRP to shoot is lacking. This has limited our ability to study the dynamic phases of reprogramming at cellular and molecular levels.

@article{kareem_plethora_2015,
	title = {\textit{{PLETHORA}} {Genes} {Control} {Regeneration} by a {Two}-{Step} {Mechanism}},
	volume = {25},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S096098221500161X},
	doi = {10.1016/j.cub.2015.02.022},
	abstract = {Regeneration, a remarkable example of developmental plasticity displayed by both plants and animals, involves successive developmental events driven in response to environmental cues. Despite decades of study on the ability of the plant tissues to regenerate a complete fertile shoot system after inductive cues, the mechanisms by which cells acquire pluripotency and subsequently regenerate complete organs remain unknown. Here, we show that three PLETHORA (PLT) genes, PLT3, PLT5, and PLT7, regulate de novo shoot regeneration in Arabidopsis by controlling two distinct developmental events. Cumulative loss of function of these three genes causes the intermediate cell mass, callus, to be incompetent to form shoot progenitors, whereas induction of PLT5 or PLT7 can render shoot regeneration hormone-independent. We further show that PLT3, PLT5, and PLT7 establish pluripotency by activating root stem cell regulators PLT1 and PLT2, as reconstitution of either PLT1 or PLT2 in the plt3; plt5-2; plt7 mutant re-established the competence to regenerate shoot progenitor cells but did not lead to the completion of shoot regeneration. PLT3, PLT5, and PLT7 additionally regulate and require the shoot-promoting factor CUP-SHAPED COTYLEDON2 (CUC2) to complete the shoot-formation program. Our findings uncouple the acquisition of competence to regenerate shoot progenitor cells from completion of shoot formation, indicating a two-step mechanism of de novo shoot regeneration that operates in all tested plant tissues irrespective of their origin. Our studies reveal intermediate developmental phases of regeneration and provide a deeper understanding into the mechanistic basis of regeneration.},
	number = {8},
	urldate = {2026-09-07},
	journal = {Current Biology},
	author = {Kareem, Abdul and Durgaprasad, Kavya and Sugimoto, Kaoru and Du, Yujuan and Pulianmackal, Ajai J. and Trivedi, Zankhana B. and Abhayadev, Pazhoor V. and Pinon, Violaine and Meyerowitz, Elliot M. and Scheres, Ben and Prasad, Kalika},
	month = apr,
	year = {2015},
	pages = {1017--1030},
}

Regeneration, a remarkable example of developmental plasticity displayed by both plants and animals, involves successive developmental events driven in response to environmental cues. Despite decades of study on the ability of the plant tissues to regenerate a complete fertile shoot system after inductive cues, the mechanisms by which cells acquire pluripotency and subsequently regenerate complete organs remain unknown. Here, we show that three PLETHORA (PLT) genes, PLT3, PLT5, and PLT7, regulate de novo shoot regeneration in Arabidopsis by controlling two distinct developmental events. Cumulative loss of function of these three genes causes the intermediate cell mass, callus, to be incompetent to form shoot progenitors, whereas induction of PLT5 or PLT7 can render shoot regeneration hormone-independent. We further show that PLT3, PLT5, and PLT7 establish pluripotency by activating root stem cell regulators PLT1 and PLT2, as reconstitution of either PLT1 or PLT2 in the plt3; plt5-2; plt7 mutant re-established the competence to regenerate shoot progenitor cells but did not lead to the completion of shoot regeneration. PLT3, PLT5, and PLT7 additionally regulate and require the shoot-promoting factor CUP-SHAPED COTYLEDON2 (CUC2) to complete the shoot-formation program. Our findings uncouple the acquisition of competence to regenerate shoot progenitor cells from completion of shoot formation, indicating a two-step mechanism of de novo shoot regeneration that operates in all tested plant tissues irrespective of their origin. Our studies reveal intermediate developmental phases of regeneration and provide a deeper understanding into the mechanistic basis of regeneration.

@article{pulianmackal_competence_2014,
	title = {Competence and regulatory interactions during regeneration in plants},
	volume = {5},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2014.00142/full},
	doi = {10.3389/fpls.2014.00142},
	abstract = {The ability to regenerate is widely exploited by multitudes of organisms ranging from unicellular bacteria to multicellular plants for their propagation and repair. But the levels of competence for regeneration vary from species to species. While variety of living cells of a plant display regeneration ability, only a few set of cells maintain their stemness in mammals. This highly pliable nature of plant cells in-terms of regeneration can be attributed to their high developmental plasticity. De novo organ initiation can be relatively easily achieved in plants by proper hormonal regulations. Elevated levels of plant hormone auxin induces the formation of proliferating mass of pluripotent cells called callus, which predominantly express lateral root meristem markers and hence is having an identity similar to lateral root primordia. Organ formation can be induced from the callus by modulating the ratio of hormones. An alternative for de novo organogenesis is by the forced expression of plant specific transcription factors. The mechanisms by which plant cells attain competence for regeneration on hormonal treatment or forced expression remain largely elusive. Recent studies have provided some insight into how the epigenetic modifications in plants affect this competence. In this review we discuss the present understanding of regenerative biology in plants and scrutinize the future prospectives of this topic. While discussing about the regeneration in the sporophyte of angiosperms which is well studied, here we outline the regenerative biology of the gametophytic phase and discuss about various strategies of regeneration that have evolved in the domain of life so that a common consensus on the entire process of regeneration can be made.},
	language = {English},
	urldate = {2026-09-07},
	journal = {Frontiers in Plant Science},
	publisher = {Frontiers},
	author = {Pulianmackal, Ajai Joseph and Kareem, Abdul VK and Durgaprasad, Kavya and Trivedi, Zankhana Bhanuprasad and Prasad, Kalika},
	month = apr,
	year = {2014},
	keywords = {Callus, De novo organ initiation, auxin, competence for regeneration, cytokinin., epigenetic modifications},
}

The ability to regenerate is widely exploited by multitudes of organisms ranging from unicellular bacteria to multicellular plants for their propagation and repair. But the levels of competence for regeneration vary from species to species. While variety of living cells of a plant display regeneration ability, only a few set of cells maintain their stemness in mammals. This highly pliable nature of plant cells in-terms of regeneration can be attributed to their high developmental plasticity. De novo organ initiation can be relatively easily achieved in plants by proper hormonal regulations. Elevated levels of plant hormone auxin induces the formation of proliferating mass of pluripotent cells called callus, which predominantly express lateral root meristem markers and hence is having an identity similar to lateral root primordia. Organ formation can be induced from the callus by modulating the ratio of hormones. An alternative for de novo organogenesis is by the forced expression of plant specific transcription factors. The mechanisms by which plant cells attain competence for regeneration on hormonal treatment or forced expression remain largely elusive. Recent studies have provided some insight into how the epigenetic modifications in plants affect this competence. In this review we discuss the present understanding of regenerative biology in plants and scrutinize the future prospectives of this topic. While discussing about the regeneration in the sporophyte of angiosperms which is well studied, here we outline the regenerative biology of the gametophytic phase and discuss about various strategies of regeneration that have evolved in the domain of life so that a common consensus on the entire process of regeneration can be made.

@article{beleyur_mathematical_2013,
	title = {A mathematical basis for plant patterning derived from physico-chemical phenomena},
	volume = {35},
	copyright = {Copyright © 2013 WILEY Periodicals, Inc.},
	issn = {1521-1878},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/bies.201200126},
	doi = {10.1002/bies.201200126},
	abstract = {The position of leaves and flowers along the stem axis generates a specific pattern, known as phyllotaxis. A growing body of evidence emerging from recent computational modeling and experimental studies suggests that regulators controlling phyllotaxis are chemical, e.g. the plant growth hormone auxin and its dynamic accumulation pattern by polar auxin transport, and physical, e.g. mechanical properties of the cell. Here we present comprehensive views on how chemical and physical properties of cells regulate the pattern of leaf initiation. We further compare different computational modeling studies to understand their scope in reproducing the observed patterns. Despite a plethora of experimental studies on phyllotaxis, understanding of molecular mechanisms of pattern initiation in plants remains fragmentary. Live imaging of growth dynamics and physicochemical properties at the shoot apex of mutants displaying stable changes from one pattern to another should provide mechanistic insights into organ initiation patterns. Editor's suggested further reading in BioEssays Computer simulation: The imaginary friend of auxin transport biology Abstract},
	language = {en},
	number = {4},
	urldate = {2026-09-07},
	journal = {BioEssays},
	author = {Beleyur, Thejasvi and Abdul Kareem, Valiya Kadavu and Shaji, Anil and Prasad, Kalika},
	year = {2013},
	keywords = {auxin, computational modeling, mechanical properties, pattern, phyllotaxis, plant, shoot meristem},
	pages = {366--376},
}

The position of leaves and flowers along the stem axis generates a specific pattern, known as phyllotaxis. A growing body of evidence emerging from recent computational modeling and experimental studies suggests that regulators controlling phyllotaxis are chemical, e.g. the plant growth hormone auxin and its dynamic accumulation pattern by polar auxin transport, and physical, e.g. mechanical properties of the cell. Here we present comprehensive views on how chemical and physical properties of cells regulate the pattern of leaf initiation. We further compare different computational modeling studies to understand their scope in reproducing the observed patterns. Despite a plethora of experimental studies on phyllotaxis, understanding of molecular mechanisms of pattern initiation in plants remains fragmentary. Live imaging of growth dynamics and physicochemical properties at the shoot apex of mutants displaying stable changes from one pattern to another should provide mechanistic insights into organ initiation patterns. Editor's suggested further reading in BioEssays Computer simulation: The imaginary friend of auxin transport biology Abstract

@article{abdul_kareem_analysis_2012,
	title = {Analysis of genetic diversity in \textit{{Acorus} calamus} populations in {South} and {North} {East} {India} using {ISSR} markers},
	volume = {40},
	issn = {0305-1978},
	url = {https://www.sciencedirect.com/science/article/pii/S030519781100192X},
	doi = {10.1016/j.bse.2011.09.012},
	abstract = {Inter simple sequence repeat (ISSR) markers were used to estimate genetic diversity among 21 samples of Acorus calamus, an endangered medicinal herb from South and North East India. Out of 100 primers screened 14 generated distinct and reproducible DNA fragments. Using these primers, 103 discernible DNA fragments were generated of which 53 (51.5\%) were polymorphic and remaining 50 (48.5\%) were monomorphic. The amplified PCR fragment size ranged from 450 to 2250 bp. Nei’s genetic diversity (h) and Shannon’s index (I) among the population were estimated as 0.2005 and 0.2946 respectively. Value for total genotype diversity among population (HT) was 0.1893 while within population diversity (HS) was found to be 0.0834. The mean coefficient of gene differentiation (GST) was as high as 0.5595 and the gene flow (Nm) was found to be 0.3937; both indicated rapid genetic differentiation among the populations of A. calamus. Analysis of molecular variance (AMOVA) indicated that 43\% was attributable to among-populations diversity and the rest (57\%) to differences within populations. The UPGMA dendrogram based on Ward’s minimum variance algorithm showed a high level genetic divergence between the populations from South and North Eastern India (∼119 linkage distance) which explains the existence of two geographically distinct populations.},
	urldate = {2026-09-07},
	journal = {Biochemical Systematics and Ecology},
	author = {Abdul Kareem, V. K. and Rajasekharan, P. E. and Ravish, B. S. and Mini, S. and Sane, Anuradha and Vasantha Kumar, T.},
	month = feb,
	year = {2012},
	keywords = {Clonal plant, Genetic diversity, ISSR, Sweet flag, UPGMA},
	pages = {156--161},
}

Inter simple sequence repeat (ISSR) markers were used to estimate genetic diversity among 21 samples of Acorus calamus, an endangered medicinal herb from South and North East India. Out of 100 primers screened 14 generated distinct and reproducible DNA fragments. Using these primers, 103 discernible DNA fragments were generated of which 53 (51.5%) were polymorphic and remaining 50 (48.5%) were monomorphic. The amplified PCR fragment size ranged from 450 to 2250 bp. Nei’s genetic diversity (h) and Shannon’s index (I) among the population were estimated as 0.2005 and 0.2946 respectively. Value for total genotype diversity among population (HT) was 0.1893 while within population diversity (HS) was found to be 0.0834. The mean coefficient of gene differentiation (GST) was as high as 0.5595 and the gene flow (Nm) was found to be 0.3937; both indicated rapid genetic differentiation among the populations of A. calamus. Analysis of molecular variance (AMOVA) indicated that 43% was attributable to among-populations diversity and the rest (57%) to differences within populations. The UPGMA dendrogram based on Ward’s minimum variance algorithm showed a high level genetic divergence between the populations from South and North Eastern India (∼119 linkage distance) which explains the existence of two geographically distinct populations.

@article{kareem_genetic_2011,
	title = {Genetic diversity and structure of the threatened anti-cancerous plant {Nothapodytes} nimmoniana as revealed by {ISSR} analysis},
	volume = {9},
	issn = {1479-263X, 1479-2621},
	url = {https://www.cambridge.org/core/journals/plant-genetic-resources/article/genetic-diversity-and-structure-of-the-threatened-anticancerous-plant-nothapodytes-nimmoniana-as-revealed-by-issr-analysis/0B202401AAB62AC9A84963330CC702D7},
	doi = {10.1017/S1479262111000803},
	abstract = {Inter simple sequence repeat markers were used to assess the genetic diversity and population genetic structure in 12 populations of Nothapodytes nimmoniana from Western Ghats of India. A total of 16 selected primers produced 103 discernible bands, with 76 (73.7\%) being polymorphic. The Nei's gene diversity (h) ranged from 0.1166 to 0.2124, with an average of 0.1518 at the population level and 0.2965 at the species level indicating high genetic diversity. The Shannon's index (I) was estimated to be 0.2189 within populations (range 0.1703–0.2947) and 0.4352 at the species level. The analysis of molecular variance showed that the genetic variation was found mainly within populations (73\%), but variance among populations was only 27\% and its value, ΦPT = 0.271, P {\textless} 0.001, implied that high genetic differentiation among populations. In addition, Nei's differentiation coefficient (GST) was found to be high (0.4882) and the gene flow (Nm) was low (0.5242), confirming the high population genetic differentiation. The unweighted pair-group method using arithmetic average clustering elicited similar results. Based on this, we propose conservation strategy for this plant species.},
	language = {en},
	number = {4},
	urldate = {2026-09-07},
	journal = {Plant Genetic Resources},
	author = {Kareem, V. K. Abdul and Rajasekharan, P. E. and Mini, S. and Kumar, T. Vasantha},
	month = dec,
	year = {2011},
	keywords = {ISSR, Nothapodytes nimmoniana, Western Ghats, anti-cancer, camptothecin, genetic differentiation, genetic diversity, population structure},
	pages = {506--514},
}

Inter simple sequence repeat markers were used to assess the genetic diversity and population genetic structure in 12 populations of Nothapodytes nimmoniana from Western Ghats of India. A total of 16 selected primers produced 103 discernible bands, with 76 (73.7%) being polymorphic. The Nei's gene diversity (h) ranged from 0.1166 to 0.2124, with an average of 0.1518 at the population level and 0.2965 at the species level indicating high genetic diversity. The Shannon's index (I) was estimated to be 0.2189 within populations (range 0.1703–0.2947) and 0.4352 at the species level. The analysis of molecular variance showed that the genetic variation was found mainly within populations (73%), but variance among populations was only 27% and its value, ΦPT = 0.271, P \textless 0.001, implied that high genetic differentiation among populations. In addition, Nei's differentiation coefficient (GST) was found to be high (0.4882) and the gene flow (Nm) was low (0.5242), confirming the high population genetic differentiation. The unweighted pair-group method using arithmetic average clustering elicited similar results. Based on this, we propose conservation strategy for this plant species.

@article{rajasekharan_optimization_2010,
	title = {Optimization of protocols for in vitro multiplication and conservation of {Nothapodytes} nimmoniana, an endangered medicinal plant},
	volume = {865},
	doi = {10.17660/ActaHortic.2010.865.5},
	abstract = {Nothapodytes nimmoniana Graham; Syn. Mappia foetida (Icacinaceae) an endangered tree species of Western Ghats of India is an excellent source of quinoline alkaloids, camptothecin (CPT), used clinically as such or after derivation as anticancer agents for the treatment of solid tumors. Development of in vitro multiplication and conservation techniques are highly desirable, as there is no reported cultivation or conservation protocols of this endangered species. MS medium with different plant growth regulators (PGRs) were tried to optimize the protocol for in vitro multiplication of this species. Among the various explants tried, only the isolated seed embryos collected from Idukki district of Kerala, showed a positive response on MS with 0.91 μM thidiazuron (TDZ), 3\% sucrose, 0.8\% agar and pH 5.8 in Standard Culture Conditions (SCC). From regenerating callus, multiple shoots were regenerated and development of somatic embryos was observed on the same medium after 3 week of incubation. After one month of incubation in TDZ medium somatic embryos developed were small, inseparable and on an average of 70 per tube and 5 mm to 15 mm long. Shoot elongation of 2–19 mm was observed on MS basal medium after one month of incubation. One mg/L IBA was ideal for root initiation of the vitro plants. Some the cultures in (SCC) were shifted to low temperature (+10°C) for in vitro conservation. Under reduced temperature and light, in vitro plants grew well (without any subculturing) even after the six months of incubation. Cultures in MS basal medium showed shoot elongation of 5–10 mm compared to MS with TDZ (3–50 mm). The interesting results of growth response of the cultures in low temperature imply that it is possible to conserve the species under low temperature for a longer period without regular subculturing. Protocols for the establishment of in vitro gene bank for these species will be discussed.},
	journal = {ISHS Acta Horticulturae},
	author = {Rajasekharan, P. E. and Abdul Kareem, V. K. and Vasantha Kumar, T.},
	year = {2010},
	pages = {53--58},
}

Nothapodytes nimmoniana Graham; Syn. Mappia foetida (Icacinaceae) an endangered tree species of Western Ghats of India is an excellent source of quinoline alkaloids, camptothecin (CPT), used clinically as such or after derivation as anticancer agents for the treatment of solid tumors. Development of in vitro multiplication and conservation techniques are highly desirable, as there is no reported cultivation or conservation protocols of this endangered species. MS medium with different plant growth regulators (PGRs) were tried to optimize the protocol for in vitro multiplication of this species. Among the various explants tried, only the isolated seed embryos collected from Idukki district of Kerala, showed a positive response on MS with 0.91 μM thidiazuron (TDZ), 3% sucrose, 0.8% agar and pH 5.8 in Standard Culture Conditions (SCC). From regenerating callus, multiple shoots were regenerated and development of somatic embryos was observed on the same medium after 3 week of incubation. After one month of incubation in TDZ medium somatic embryos developed were small, inseparable and on an average of 70 per tube and 5 mm to 15 mm long. Shoot elongation of 2–19 mm was observed on MS basal medium after one month of incubation. One mg/L IBA was ideal for root initiation of the vitro plants. Some the cultures in (SCC) were shifted to low temperature (+10°C) for in vitro conservation. Under reduced temperature and light, in vitro plants grew well (without any subculturing) even after the six months of incubation. Cultures in MS basal medium showed shoot elongation of 5–10 mm compared to MS with TDZ (3–50 mm). The interesting results of growth response of the cultures in low temperature imply that it is possible to conserve the species under low temperature for a longer period without regular subculturing. Protocols for the establishment of in vitro gene bank for these species will be discussed.