@article{anjam_single-cell_2026,
	title = {Single-cell laser ablation uncovers the blueprint of plant development},
	issn = {1360-1385},
	url = {https://www.sciencedirect.com/science/article/pii/S1360138526001329},
	doi = {10.1016/j.tplants.2026.04.029},
	abstract = {Understanding how positional information within plant tissues shapes developmental programs in real time has long remained a challenge due to technical limitations in precisely accessing and manipulating defined cellular domains within complex tissues. Recent advances in single-cell laser ablation, particularly when combined with confocal microscopy, now allow precise spatiotemporal perturbation of selected cells. This technology has enabled researchers to dissect cellular functions, communication dynamics, and mechanical responses with unprecedented accuracy. Here, we review how laser ablation has emerged as a transformative approach in plant biology, from unraveling the signaling networks governing meristem maintenance and root patterning to modeling wound responses and immune activation.},
	urldate = {2026-05-29},
	journal = {Trends in Plant Science},
	author = {Anjam, Muhammad S. and Di Fino, Luciano Martín and Ma, Xuemin and Marhavý, Peter},
	month = may,
	year = {2026},
	keywords = {phytohormone crosstalk, single-cell ablation, tissue regeneration, wound signaling},
}

Understanding how positional information within plant tissues shapes developmental programs in real time has long remained a challenge due to technical limitations in precisely accessing and manipulating defined cellular domains within complex tissues. Recent advances in single-cell laser ablation, particularly when combined with confocal microscopy, now allow precise spatiotemporal perturbation of selected cells. This technology has enabled researchers to dissect cellular functions, communication dynamics, and mechanical responses with unprecedented accuracy. Here, we review how laser ablation has emerged as a transformative approach in plant biology, from unraveling the signaling networks governing meristem maintenance and root patterning to modeling wound responses and immune activation.

@article{ma_ca2_2025,
	title = {Ca2+ waves and ethylene/{JA} crosstalk orchestrate wound responses in {Arabidopsis} roots},
	volume = {26},
	issn = {1469-221X},
	url = {https://www.embopress.org/doi/full/10.1038/s44319-025-00471-z},
	doi = {10.1038/s44319-025-00471-z},
	abstract = {Wounding triggers complex and multi-faceted responses in plants. Among these, calcium (Ca2+) waves serve as an immediate and localized response to strong stimuli, such as nematode infection or laser ablation. Here, we investigate the propagation patterns of Ca2+ waves induced by laser ablation and observe that glutamate-receptor-like channels (GLR3.3/GLR3.6), the stretch-activated anion channel MSL10, and the mechanosensitive Ca2+-permeable channels MCA1/MCA2 influence this process. These channels contribute to ethylene-associated signaling pathways, potentially through the WRKY33-ACS6 regulatory network. Furthermore, our findings show that ACC/ethylene signaling modulates Ca2+ wave propagation following laser ablation. Ethylene perception and synthesis at the site of damage regulate the local jasmonate response, which displays tissue-specific patterns upon laser ablation. Overall, our data provide new insights into the molecular and cellular processes underlying plant responses to localized damage, highlighting the roles of specific ion channels and hormone signaling pathways in shaping these responses in Arabidopsis roots.},
	number = {12},
	urldate = {2025-06-27},
	journal = {EMBO reports},
	publisher = {John Wiley \& Sons, Ltd},
	author = {Ma, Xuemin and Hasan, M Shamim and Anjam, Muhammad Shahzad and Mahmud, Sakil and Bhattacharyya, Sabarna and Vothknecht, Ute C and Mendy, Badou and Grundler, Florian M W and Marhavý, Peter},
	month = jun,
	year = {2025},
	note = {Num Pages: 3203},
	keywords = {Ca2+ Wave, Ethylene, Jasmonate, Laser Ablation},
	pages = {3187--3203},
}

Wounding triggers complex and multi-faceted responses in plants. Among these, calcium (Ca2+) waves serve as an immediate and localized response to strong stimuli, such as nematode infection or laser ablation. Here, we investigate the propagation patterns of Ca2+ waves induced by laser ablation and observe that glutamate-receptor-like channels (GLR3.3/GLR3.6), the stretch-activated anion channel MSL10, and the mechanosensitive Ca2+-permeable channels MCA1/MCA2 influence this process. These channels contribute to ethylene-associated signaling pathways, potentially through the WRKY33-ACS6 regulatory network. Furthermore, our findings show that ACC/ethylene signaling modulates Ca2+ wave propagation following laser ablation. Ethylene perception and synthesis at the site of damage regulate the local jasmonate response, which displays tissue-specific patterns upon laser ablation. Overall, our data provide new insights into the molecular and cellular processes underlying plant responses to localized damage, highlighting the roles of specific ion channels and hormone signaling pathways in shaping these responses in Arabidopsis roots.

@article{di_fino_cellular_2025,
	title = {Cellular damage triggers mechano-chemical control of cell wall dynamics and patterned cell divisions in plant healing},
	volume = {60},
	issn = {1534-5807},
	url = {https://www.sciencedirect.com/science/article/pii/S1534580724007718},
	doi = {10.1016/j.devcel.2024.12.032},
	abstract = {Reactivation of cell division is crucial for the regeneration of damaged tissues, which is a fundamental process across all multicellular organisms. However, the mechanisms underlying the activation of cell division in plants during regeneration remain poorly understood. Here, we show that single-cell endodermal ablation generates a transient change in the local mechanical pressure on neighboring pericycle cells to activate patterned cell division that is crucial for tissue regeneration in Arabidopsis roots. Moreover, we provide strong evidence that this process relies on the phytohormone ethylene. Thus, our results highlight a previously unrecognized role of mechano-chemical control in patterned cell division during regeneration in plants.},
	number = {10},
	urldate = {2025-05-23},
	journal = {Developmental Cell},
	author = {Di Fino, Luciano Martín and Anjam, Muhammad Shahzad and Besten, Maarten and Mentzelopoulou, Andriani and Papadakis, Vassilis and Zahid, Nageena and Baez, Luis Alonso and Trozzi, Nicola and Majda, Mateusz and Ma, Xuemin and Hamann, Thorsten and Sprakel, Joris and Moschou, Panagiotis N. and Smith, Richard S. and Marhavý, Peter},
	month = may,
	year = {2025},
	keywords = {cell division, cell wall, ethylene, mechanobiology, pectin, regeneration, single-cell laser ablation, xylem-pole-pericycle},
	pages = {1411--1422.e6},
}

Reactivation of cell division is crucial for the regeneration of damaged tissues, which is a fundamental process across all multicellular organisms. However, the mechanisms underlying the activation of cell division in plants during regeneration remain poorly understood. Here, we show that single-cell endodermal ablation generates a transient change in the local mechanical pressure on neighboring pericycle cells to activate patterned cell division that is crucial for tissue regeneration in Arabidopsis roots. Moreover, we provide strong evidence that this process relies on the phytohormone ethylene. Thus, our results highlight a previously unrecognized role of mechano-chemical control in patterned cell division during regeneration in plants.

@article{mazumdar_damage_2025,
	title = {Damage activates \textit{{EXG1}} and \textit{{RLP44}} to suppress vascular differentiation during regeneration in \textit{{Arabidopsis}}},
	volume = {6},
	issn = {2590-3462},
	url = {https://www.sciencedirect.com/science/article/pii/S2590346225000185},
	doi = {10.1016/j.xplc.2025.101256},
	abstract = {Plants possess remarkable regenerative abilities to form de novo vasculature after damage and in response to pathogens that invade and withdraw nutrients. To identify common factors that affect vascular formation upon stress, we searched for Arabidopsis thaliana genes differentially expressed upon Agrobacterium infection, nematode infection, and plant grafting. One such gene is cell wall-related and highly induced by all three stresses, which we named ENHANCED XYLEM AND GRAFTING1 (EXG1), since its mutations promote ectopic xylem formation in a vascular cell induction system and enhance graft formation. Further observations revealed that exg1 mutants show inhibited cambium development and callus formation but enhanced tissue attachment, syncytium size, phloem reconnection, and xylem formation. Given that brassinosteroids also promote xylem differentiation, we analyzed brassinosteroid-related genes and found that mutations in RLP44 encoding a receptor-like protein cause similar regeneration-related phenotypes as mutations in EXG1. Like EXG1, RLP44 expression is also induced by grafting and wounding. Mutations in EXG1 and RLP44 affect the expression of many genes in common, including those related to cell walls and genes important for vascular regeneration. Our results suggest that EXG1 integrates information from wounding or pathogen stress and functions with RLP44 to suppress vascular differentiation during regeneration and healing.},
	number = {4},
	urldate = {2025-04-22},
	journal = {Plant Communications},
	author = {Mazumdar, Shamik and Augstein, Frauke and Zhang, Ai and Musseau, Constance and Anjam, Muhammad Shahzad and Marhavy, Peter and Melnyk, Charles W.},
	month = apr,
	year = {2025},
	keywords = {Cell wall, Grafting, Regeneration, Stress, Wounding, Xylem, cell wall, grafting, regeneration, stress, wounding, xylem},
	pages = {101256},
}

Plants possess remarkable regenerative abilities to form de novo vasculature after damage and in response to pathogens that invade and withdraw nutrients. To identify common factors that affect vascular formation upon stress, we searched for Arabidopsis thaliana genes differentially expressed upon Agrobacterium infection, nematode infection, and plant grafting. One such gene is cell wall-related and highly induced by all three stresses, which we named ENHANCED XYLEM AND GRAFTING1 (EXG1), since its mutations promote ectopic xylem formation in a vascular cell induction system and enhance graft formation. Further observations revealed that exg1 mutants show inhibited cambium development and callus formation but enhanced tissue attachment, syncytium size, phloem reconnection, and xylem formation. Given that brassinosteroids also promote xylem differentiation, we analyzed brassinosteroid-related genes and found that mutations in RLP44 encoding a receptor-like protein cause similar regeneration-related phenotypes as mutations in EXG1. Like EXG1, RLP44 expression is also induced by grafting and wounding. Mutations in EXG1 and RLP44 affect the expression of many genes in common, including those related to cell walls and genes important for vascular regeneration. Our results suggest that EXG1 integrates information from wounding or pathogen stress and functions with RLP44 to suppress vascular differentiation during regeneration and healing.

@article{shahid_copper-treated_2023,
	title = {Copper-{Treated} {Environmentally} {Friendly} {Antipathogenic} {Cotton} {Fabric} with {Modified} {Reactive} {Blue} 4 {Dye} to {Improve} {Its} {Antibacterial} and {Aesthetic} {Properties}},
	volume = {13},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2079-6412},
	url = {https://www.mdpi.com/2079-6412/13/1/133},
	doi = {10.3390/coatings13010133},
	abstract = {The objectives of the present study were to develop an environmentally friendly, low-price, easy, and fast method for developing antipathogenic (antibacterial, antifungal, and antiviral) cuprous-oxide-coated multifunctional fabrics. The fabrics were first sensitized with citric acid, and then Cu2O particles were formed using the Fehling solution method. The cuprous oxide particles were then applied to the cotton fabrics. To create the Cu2O particles, three different kinds of reducing agents with varying concentrations were used. SEM, dynamic light scattering, FTIR, EDS, and XRD were used to examine the surface morphologies and metal presences. In the second step, a reactive antibacterial dye was made (by reacting Reactive Blue 4 with triclosan). The molecular structure of the modified dye was confirmed with FTIR. The resultant antibacterial dye was applied on the copper-treated cotton fabrics in accordance with the exhaust dyeing protocol. The dyed fabrics were characterized through the colorimetric data (L*, a*, b*, C, H, and K/S), levelness of dye, fastness properties as well as exhaustion and fixation rates. Cuprous-oxide-coated fabrics were tested for antipathogenic activity using quantitative and qualitative measurement results. The fabrics treated with cuprous oxide particles reduced with sodium hydrosulfite at 1 g/L seemed to have the highest antipathogenic effect. Moreover, the versatility of the hygienically developed bioactive fabrics in terms of their comfort properties such as air permeability and stiffness were investigated. Finally, the coating’s durability was confirmed by evaluating its antibacterial properties and performing an SEM analysis after laundry.},
	language = {en},
	number = {1},
	urldate = {2024-08-30},
	journal = {Coatings},
	publisher = {Multidisciplinary Digital Publishing Institute},
	author = {Shahid, Muhammad and Ali, Azam and Zahid, Nageena and Anjam, Muhammad Shahzad and Militky, Jiri and Wiener, Jakub and Palanisamy, Sundaramoorthy and Tomkova, Blanka},
	month = jan,
	year = {2023},
	note = {Number: 1},
	keywords = {antimicrobial, color analysis, cuprous oxide particles, hospital-acquired infections, medical textiles},
	pages = {133},
}

The objectives of the present study were to develop an environmentally friendly, low-price, easy, and fast method for developing antipathogenic (antibacterial, antifungal, and antiviral) cuprous-oxide-coated multifunctional fabrics. The fabrics were first sensitized with citric acid, and then Cu2O particles were formed using the Fehling solution method. The cuprous oxide particles were then applied to the cotton fabrics. To create the Cu2O particles, three different kinds of reducing agents with varying concentrations were used. SEM, dynamic light scattering, FTIR, EDS, and XRD were used to examine the surface morphologies and metal presences. In the second step, a reactive antibacterial dye was made (by reacting Reactive Blue 4 with triclosan). The molecular structure of the modified dye was confirmed with FTIR. The resultant antibacterial dye was applied on the copper-treated cotton fabrics in accordance with the exhaust dyeing protocol. The dyed fabrics were characterized through the colorimetric data (L*, a*, b*, C, H, and K/S), levelness of dye, fastness properties as well as exhaustion and fixation rates. Cuprous-oxide-coated fabrics were tested for antipathogenic activity using quantitative and qualitative measurement results. The fabrics treated with cuprous oxide particles reduced with sodium hydrosulfite at 1 g/L seemed to have the highest antipathogenic effect. Moreover, the versatility of the hygienically developed bioactive fabrics in terms of their comfort properties such as air permeability and stiffness were investigated. Finally, the coating’s durability was confirmed by evaluating its antibacterial properties and performing an SEM analysis after laundry.

@article{manzoor_photosynthetic_2022,
	title = {Photosynthetic {Efficiency} and {Antioxidant} {Defense} {Potential} are {Key} {Players} in {Inducing} {Drought} {Tolerance} in {Transgenic} {Tobacco} {Plants} {Over}-{Expressing} {AVP1}},
	volume = {41},
	issn = {1435-8107},
	url = {https://doi.org/10.1007/s00344-021-10464-6},
	doi = {10.1007/s00344-021-10464-6},
	abstract = {Plants have developed a number of physiological, biochemical, and molecular strategies to overcome water deficit conditions. Arabidopsis vacuolar pyrophosphatase 1 (AVP1) can enhance stress tolerance in plants through ion homeostasis, redox balance, and photosynthetic activity. In the present study, three transgenic tobacco lines overexpressing AVP1 gene were compared with a wild type (WT) line to assess the role of AVP1 in inducing drought tolerance. For this purpose, four-week old tobacco plants were subjected to cyclic drought for three weeks and were evaluated for different physio-biochemical parameters. Drought stress reduced shoot and root dry mass (85\% and 73\%), relative water content (55\%), K+ accumulation (42\%), and Photosystem-II (PSII) efficiency (27\%), but this effect was less on transgenic tobacco lines of AVP1 (L2, L3). Drought stress decreased performance index (PIABS) by 48\% in WT plants, which is linked with substantial increase in specific energy fluxes through PSII per active reaction center (ABS/RC, TR0/RC) and cause a decrease in electron transport (ET0/RC) by 47\%, that resulted in damage of donor end of PSII. However, AVP1 transgenic line L3 showed minimum decrease in quantum efficiency of PSII (3\%) and PIABS (12\%) due to lesser drought-induced oxidative damage and having higher catalase activity (96\%). As compared to control plants, drought-stressed WT plants significantly enhanced hydrogen peroxide and malondialdehyde production by 101\% and 98\%, respectively. However, transgenic lines particularly L2 and L3 had lower levels of H2O2 (26\% and 14\%) and MDA (56\% and 16\%), which were positively associated with higher activities of catalase. In conclusion, AVP1 gene helped to maintain water and K+ homeostasis, which in turn affected the redox balance and PSII structural and functional stability.},
	language = {en},
	number = {7},
	urldate = {2024-08-30},
	journal = {Journal of Plant Growth Regulation},
	author = {Manzoor, Hamid and Anjam, Muhammad Shahzad and Saeed, Fozia and Rasul, Sumaira and Yousaf, Saira and Kirn, Ayesha and Qureshi, Muhammad Kamran and Zafar, Zafar Ullah and Ashraf, Muhammad and Athar, Habib-ur-Rehman},
	month = oct,
	year = {2022},
	keywords = {Arabidopsis vacuolar pyrophosphatase, Catalase, Drought, JIP-test, Photosystem-II, Reactive oxygen species},
	pages = {2653--2668},
}

Plants have developed a number of physiological, biochemical, and molecular strategies to overcome water deficit conditions. Arabidopsis vacuolar pyrophosphatase 1 (AVP1) can enhance stress tolerance in plants through ion homeostasis, redox balance, and photosynthetic activity. In the present study, three transgenic tobacco lines overexpressing AVP1 gene were compared with a wild type (WT) line to assess the role of AVP1 in inducing drought tolerance. For this purpose, four-week old tobacco plants were subjected to cyclic drought for three weeks and were evaluated for different physio-biochemical parameters. Drought stress reduced shoot and root dry mass (85% and 73%), relative water content (55%), K+ accumulation (42%), and Photosystem-II (PSII) efficiency (27%), but this effect was less on transgenic tobacco lines of AVP1 (L2, L3). Drought stress decreased performance index (PIABS) by 48% in WT plants, which is linked with substantial increase in specific energy fluxes through PSII per active reaction center (ABS/RC, TR0/RC) and cause a decrease in electron transport (ET0/RC) by 47%, that resulted in damage of donor end of PSII. However, AVP1 transgenic line L3 showed minimum decrease in quantum efficiency of PSII (3%) and PIABS (12%) due to lesser drought-induced oxidative damage and having higher catalase activity (96%). As compared to control plants, drought-stressed WT plants significantly enhanced hydrogen peroxide and malondialdehyde production by 101% and 98%, respectively. However, transgenic lines particularly L2 and L3 had lower levels of H2O2 (26% and 14%) and MDA (56% and 16%), which were positively associated with higher activities of catalase. In conclusion, AVP1 gene helped to maintain water and K+ homeostasis, which in turn affected the redox balance and PSII structural and functional stability.

@incollection{anjam_rna_2022,
	address = {New York, NY},
	series = {Methods in {Molecular} {Biology}},
	title = {{RNA} {Isolation} from {Nematode}-{Induced} {Feeding} {Sites} in {Arabidopsis} {RootsRoots} {Using} {Laser} {Capture} {Microdissection}},
	isbn = {978-1-07-162297-1},
	url = {https://doi.org/10.1007/978-1-0716-2297-1_22},
	abstract = {Nematodes are diverse multicellular organisms that are most abundantly found in the soil. Most nematodes are free-living and feed on a range of organisms. Based on their feeding habits, soil nematodes can be classified into four groups: bacterial, omnivorous, fungal, and plant-feeding. Plant-parasitic nematodes (PPNs) are a serious threat to global food security, causing substantial losses to the agricultural sector. Root-knot and cyst nematodes are the most important of PPNs, significantly limiting the yield of commercial crops such as sugar beet, mustard, and cauliflower. The life cycle of these nematodes consists of four molting stages (J1–J4) that precede adulthood. Nonetheless, only second-stage juveniles (J2), which hatch from eggs, are infective worms that can parasitize the host’s roots. The freshly hatched juveniles (J2) of beet cyst nematode, Heterodera schachtii, establish a permanent feeding site inside the roots of the host plant. A cocktail of proteinaceous secretions is injected into a selected cell which later develops into a syncytium via local cell wall dissolution of several hundred neighboring cells. The formation of syncytium is accompanied by massive transcriptional, metabolic, and proteomic changes inside the host tissues. It creates a metabolic sink in which solutes are translocated to feed the nematodes throughout their life cycle. Deciphering the molecular signaling cascades during syncytium establishment is thus essential in studying the plant-nematode interactions and ensuring sustainability in agricultural practices. However, isolating RNA, protein, and metabolites from syncytial cells remains challenging. Extensive use of laser capture microdissection (LCM) in animal and human tissues has shown this approach to be a powerful technique for isolating a single cell from complex tissues. Here, we describe a simplified protocol for Arabidopsis-Heterodera schachtii infection assays, which is routinely applied in several plant-nematode laboratories. Next, we provide a detailed protocol for isolating high-quality RNA from syncytial cells induced by Heterodera schachtii in the roots of Arabidopsis thaliana plants.},
	language = {en},
	urldate = {2022-04-29},
	booktitle = {Environmental {Responses} in {Plants}: {Methods} and {Protocols}},
	publisher = {Springer US},
	author = {Anjam, Muhammad Shahzad and Siddique, Shahid and Marhavý, Peter},
	editor = {Duque, Paula and Szakonyi, Dóra},
	year = {2022},
	keywords = {Arabidopsis root dissection, Laser capture dissection, Plant-nematode infection, RNA extraction, Syncytial cell isolation},
	pages = {313--324},
}

Nematodes are diverse multicellular organisms that are most abundantly found in the soil. Most nematodes are free-living and feed on a range of organisms. Based on their feeding habits, soil nematodes can be classified into four groups: bacterial, omnivorous, fungal, and plant-feeding. Plant-parasitic nematodes (PPNs) are a serious threat to global food security, causing substantial losses to the agricultural sector. Root-knot and cyst nematodes are the most important of PPNs, significantly limiting the yield of commercial crops such as sugar beet, mustard, and cauliflower. The life cycle of these nematodes consists of four molting stages (J1–J4) that precede adulthood. Nonetheless, only second-stage juveniles (J2), which hatch from eggs, are infective worms that can parasitize the host’s roots. The freshly hatched juveniles (J2) of beet cyst nematode, Heterodera schachtii, establish a permanent feeding site inside the roots of the host plant. A cocktail of proteinaceous secretions is injected into a selected cell which later develops into a syncytium via local cell wall dissolution of several hundred neighboring cells. The formation of syncytium is accompanied by massive transcriptional, metabolic, and proteomic changes inside the host tissues. It creates a metabolic sink in which solutes are translocated to feed the nematodes throughout their life cycle. Deciphering the molecular signaling cascades during syncytium establishment is thus essential in studying the plant-nematode interactions and ensuring sustainability in agricultural practices. However, isolating RNA, protein, and metabolites from syncytial cells remains challenging. Extensive use of laser capture microdissection (LCM) in animal and human tissues has shown this approach to be a powerful technique for isolating a single cell from complex tissues. Here, we describe a simplified protocol for Arabidopsis-Heterodera schachtii infection assays, which is routinely applied in several plant-nematode laboratories. Next, we provide a detailed protocol for isolating high-quality RNA from syncytial cells induced by Heterodera schachtii in the roots of Arabidopsis thaliana plants.

@misc{zubair_ishaq_effect_2020,
	title = {Effect of {Heritability}, {Genetic} {Advance} and {Correlation} on {Yield} {Contributing} {Traits} in {Upland} {Cotton}.},
	url = {chrome-extension://efaidnbmnnnibpcajpcglclefindmkaj/https://dergipark.org.tr/en/download/article-file/961804},
	abstract = {This research was planned to study the heritability (broad sense), correlation, genetic advance and behavior of different characters in segregating population of upland cotton. The material consists of segregating population of fourteen crosses along with their seven parents. Parental varieties and segregating population show significant difference for all traits under the study. Plant height, ginning out turn (GOT), bolls per plant and yield per plant showed heritability ranging from 78.9 to 27.3. Significant genotypic correlation of yield with plant height was 0.698, bolls per plant was 0.930, GOT was 0.692, fiber strength was 0.548 and with fiber fineness was 0.435. Phenotypic correlation of yield per plant with plant height was 0.520, boll per plant was 0.894 and GOT was 0.476. It can be suggested that plant height, GOT and bolls per plant are important yield contributing traits as they are positively correlated with seed cotton yield per plant. High value for bolls per plant, GOT and yield per plant was recorded in BH-167 × V4 and CIM-534 × V4, which can be utilized in future breeding program.},
	urldate = {2024-08-30},
	author = {Zubair Ishaq, Muhammad and Hassan, Ali and Munir, Sana and Shahzad, Ahmad and Anjam, Muhammad Shahzad and Bhutta, Muhammad Asim and Kamran Qureshi},
	month = feb,
	year = {2020},
}

This research was planned to study the heritability (broad sense), correlation, genetic advance and behavior of different characters in segregating population of upland cotton. The material consists of segregating population of fourteen crosses along with their seven parents. Parental varieties and segregating population show significant difference for all traits under the study. Plant height, ginning out turn (GOT), bolls per plant and yield per plant showed heritability ranging from 78.9 to 27.3. Significant genotypic correlation of yield with plant height was 0.698, bolls per plant was 0.930, GOT was 0.692, fiber strength was 0.548 and with fiber fineness was 0.435. Phenotypic correlation of yield per plant with plant height was 0.520, boll per plant was 0.894 and GOT was 0.476. It can be suggested that plant height, GOT and bolls per plant are important yield contributing traits as they are positively correlated with seed cotton yield per plant. High value for bolls per plant, GOT and yield per plant was recorded in BH-167 × V4 and CIM-534 × V4, which can be utilized in future breeding program.

@article{anjam_host_2020,
	title = {Host factors influence the sex of nematodes parasitizing roots of},
	volume = {43},
	copyright = {© 2019 The Authors. Plant, Cell \& Environment published by Wiley Periodicals, Inc.},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.13728},
	doi = {10.1111/pce.13728},
	abstract = {Plant-parasitic cyst nematodes induce hypermetabolic syncytial nurse cells in the roots of their host plants. Syncytia are their only food source. Cyst nematodes are sexually dimorphic, with their differentiation into male or female strongly influenced by host environmental conditions. Under favourable conditions with plenty of nutrients, more females develop, whereas mainly male nematodes develop under adverse conditions such as in resistant plants. Here, we developed and validated a method to predict the sex of beet cyst nematode (Heterodera schachtii) during the early stages of its parasitism in the host plant Arabidopsis thaliana. We collected root segments containing male-associated syncytia (MAS) or female-associated syncytia (FAS), isolated syncytial cells by laser microdissection, and performed a comparative transcriptome analysis. Genes belonging to categories of defence, nutrient deficiency, and nutrient starvation were over-represented in MAS as compared with FAS. Conversely, gene categories related to metabolism, modification, and biosynthesis of cell walls were over-represented in FAS. We used β-glucuronidase analysis, qRT-PCR, and loss-of-function mutants to characterize FAS- and MAS-specific candidate genes. Our results demonstrate that various plant-based factors, including immune response, nutrient availability, and structural modifications, influence the sexual fate of the cyst nematodes.},
	language = {en},
	number = {5},
	urldate = {2024-08-30},
	journal = {Plant, Cell \& Environment},
	author = {Anjam, Muhammad Shahzad and Shah, Syed Jehangir and Matera, Christiane and Różańska, Elżbieta and Sobczak, Miroslaw and Siddique, Shahid and Grundler, Florian M. W.},
	year = {2020},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.13728},
	keywords = {cyst nematodes, environmental sex determination, host–plant interaction, plant–nematode interaction},
	pages = {1160--1174},
}

Plant-parasitic cyst nematodes induce hypermetabolic syncytial nurse cells in the roots of their host plants. Syncytia are their only food source. Cyst nematodes are sexually dimorphic, with their differentiation into male or female strongly influenced by host environmental conditions. Under favourable conditions with plenty of nutrients, more females develop, whereas mainly male nematodes develop under adverse conditions such as in resistant plants. Here, we developed and validated a method to predict the sex of beet cyst nematode (Heterodera schachtii) during the early stages of its parasitism in the host plant Arabidopsis thaliana. We collected root segments containing male-associated syncytia (MAS) or female-associated syncytia (FAS), isolated syncytial cells by laser microdissection, and performed a comparative transcriptome analysis. Genes belonging to categories of defence, nutrient deficiency, and nutrient starvation were over-represented in MAS as compared with FAS. Conversely, gene categories related to metabolism, modification, and biosynthesis of cell walls were over-represented in FAS. We used β-glucuronidase analysis, qRT-PCR, and loss-of-function mutants to characterize FAS- and MAS-specific candidate genes. Our results demonstrate that various plant-based factors, including immune response, nutrient availability, and structural modifications, influence the sexual fate of the cyst nematodes.

@article{hasan_salicylic_2020,
	title = {Salicylic acid supplementation alleviated the adverse effects of salinity stress in {Spinacia} oleracea by improved antioxidative defence system},
	url = {https://www.torrossa.com/en/resources/an/4790799},
	doi = {10.12871/00021857202045},
	abstract = {Purchase online the PDF of Salicylic acid supplementation alleviated the adverse effects of salinity stress in Spinacia oleracea by improved antioxidative defence system, Hasan, I.,Rasul, S.,Bukhat, S.,Qureshi, M. K.,Aslam, K. - Pisa University Press - Article},
	language = {en},
	urldate = {2024-08-30},
	journal = {Agrochimica : International Journal of Plant Chemistry, Soil Science and Plant Nutrition of the University of Pisa : 64, 4, 2020},
	publisher = {Pisa University Press},
	author = {Hasan, I. and Rasul, S. and Bukhat, S. and Qureshi, M. K. and Aslam, K. and Noreen, S. and Anjam, M. S. and Athar, H.-u-R. and Manzoor, H.},
	year = {2020},
	pages = {379--395},
}

Purchase online the PDF of Salicylic acid supplementation alleviated the adverse effects of salinity stress in Spinacia oleracea by improved antioxidative defence system, Hasan, I.,Rasul, S.,Bukhat, S.,Qureshi, M. K.,Aslam, K. - Pisa University Press - Article

@misc{munir_genetic_2019,
	title = {Genetic {Dissection} of {Interspecific} and {Intraspecific} {Hybrids} of {Cotton} for {Morpho}-{Yield} and {Fiber} {Traits} using {Multivariate} {Analysis}},
	url = {https://www.proquest.com/openview/f532242b07e5a7a10ee3912afae2f98e/1?cbl=616518&pq-origsite=gscholar&parentSessionId=PY5aNSs2kJmEzlzqCOK2mW6L3YvSkw0ShO3pneCGncs%3D},
	abstract = {To estimate level of genetic diversity various cotton genotypes, inter and intraspecific hybrids were assessed for yield, yield contributing and fiber traits using various multivariate analysis such as principle component analysis and linkage cluster analysis. Principle component analysis (PCA) exhibited that first four PC out of nineteen PC, with eigen value {\textgreater}1, contributed about 80.326 \% of total variability. Positive contribution towards PC1 was given by seed traits such as lint/seed, seed weight/seed, boll weight, seed index and seed cotton/seed. In biplot analysis, intraspecific hybrids and their parents were present very close to each other while interspecific hybrids, their parent and exotic line were unsimilar and far apart from intraspecific
hybrids. Results of linkage cluster analysis (LCA) revealed that among four clusters, performance of genotypes in cluster 3 was superior. PCA and LCA showed that interspecific hybrids showed highest diversity from intraspecific hybrids and concluded that intraspecific hybrids had narrow genetic basis, which can be altered
by using interspecific hybrids or exotic lines. These genotypes can be exploited for variety development with enhanced level of diversity, fiber quality and seed cotton yield.},
	language = {en},
	urldate = {2024-08-30},
	author = {Munir, Sana and Qureshi, Muhammad Kamran and Shahzad, Ahmad Naeem and Nawaz, Ismat and Anjam, Muhammad Shahzad and Rasul, Sumaira and Zulfiqar, Muhammad Asif},
	month = jun,
	year = {2019},
}

To estimate level of genetic diversity various cotton genotypes, inter and intraspecific hybrids were assessed for yield, yield contributing and fiber traits using various multivariate analysis such as principle component analysis and linkage cluster analysis. Principle component analysis (PCA) exhibited that first four PC out of nineteen PC, with eigen value \textgreater1, contributed about 80.326 % of total variability. Positive contribution towards PC1 was given by seed traits such as lint/seed, seed weight/seed, boll weight, seed index and seed cotton/seed. In biplot analysis, intraspecific hybrids and their parents were present very close to each other while interspecific hybrids, their parent and exotic line were unsimilar and far apart from intraspecific hybrids. Results of linkage cluster analysis (LCA) revealed that among four clusters, performance of genotypes in cluster 3 was superior. PCA and LCA showed that interspecific hybrids showed highest diversity from intraspecific hybrids and concluded that intraspecific hybrids had narrow genetic basis, which can be altered by using interspecific hybrids or exotic lines. These genotypes can be exploited for variety development with enhanced level of diversity, fiber quality and seed cotton yield.

@article{mehmood_physical_2019,
	title = {Physical and chemical mutagens improved \textit{{Sporotrichum} thermophile}, strain {ST20} for enhanced {Phytase} activity},
	volume = {26},
	issn = {1319-562X},
	url = {https://www.sciencedirect.com/science/article/pii/S1319562X1930124X},
	doi = {10.1016/j.sjbs.2019.07.006},
	abstract = {Objective
Phosphorous is an essential micronutrient of plants and involved in critical biological functions. In nature, phosphorous is mostly present in immobilized inorganic mineral and in the fixed organic form including phytic acid and phosphoesteric compounds. However, the bioavailability of bound phosphorous could be enhanced by the use of phosphate solubilizing microorganisms such as bacteria and fungi. The phytases are widespread in an environment and have been isolated from different sources comprising bacteria and fungi.
Methodology
In current studies, we show the successful use of gamma rays and EMS (Ethyl Methane Sulphonate) mutagenesis for enhanced activity of phytases in a fungal strain Sporotrichum thermophile.
Results
We report an improved strain ST2 that could produce a clear halo zone around the colony, up to 24 mm. The maximum enzymatic activity was found of 382 U/mL on pH 5.5. However, the phytase activity was improved to 387 U/ml at 45 °C. We also report that the mutants produced through EMS showed the greater potential for phytase production.
Conclusion
The current study highlights the potential of EMS mutagenesis for strain improvement over physical mutagens.},
	number = {7},
	urldate = {2024-08-30},
	journal = {Saudi Journal of Biological Sciences},
	author = {Mehmood, Asim and Baneen, Umal and Zaheer, Ahmad and Wasim Sajid, Muhammad and Hussain, Abrar and Saleem, Shahzad and Yousafi, Qudsia and Rashid, Hamid and Riaz, Hassan and Ihsan, Awais and Jamil, Farrukh and Sajjad, Yasar and Zahid, Nageena and Anjam, Muhammad Shahzad and Arshad, Muhammad and Mirza, Zeenat and Karim, Sajjad and Rasool, Mahmood},
	month = nov,
	year = {2019},
	keywords = {EMS mutagenesis, Fungus, Gamma rays, Phosphate solubilizer},
	pages = {1485--1491},
}

Objective Phosphorous is an essential micronutrient of plants and involved in critical biological functions. In nature, phosphorous is mostly present in immobilized inorganic mineral and in the fixed organic form including phytic acid and phosphoesteric compounds. However, the bioavailability of bound phosphorous could be enhanced by the use of phosphate solubilizing microorganisms such as bacteria and fungi. The phytases are widespread in an environment and have been isolated from different sources comprising bacteria and fungi. Methodology In current studies, we show the successful use of gamma rays and EMS (Ethyl Methane Sulphonate) mutagenesis for enhanced activity of phytases in a fungal strain Sporotrichum thermophile. Results We report an improved strain ST2 that could produce a clear halo zone around the colony, up to 24 mm. The maximum enzymatic activity was found of 382 U/mL on pH 5.5. However, the phytase activity was improved to 387 U/ml at 45 °C. We also report that the mutants produced through EMS showed the greater potential for phytase production. Conclusion The current study highlights the potential of EMS mutagenesis for strain improvement over physical mutagens.

@article{radakovic_arabidopsis_2018,
	title = {Arabidopsis {HIPP27} is a host susceptibility gene for the beet cyst nematode {Heterodera} schachtii},
	volume = {19},
	copyright = {© 2018 UNIVERSITY BONN. MOLECULAR PLANT PATHOLOGY © 2018 BSPP AND JOHN WILEY \& SONS LTD},
	issn = {1364-3703},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/mpp.12668},
	doi = {10.1111/mpp.12668},
	abstract = {Sedentary plant-parasitic cyst nematodes are obligate biotrophs that infect the roots of their host plant. Their parasitism is based on the modification of root cells to form a hypermetabolic syncytium from which the nematodes draw their nutrients. The aim of this study was to identify nematode susceptibility genes in Arabidopsis thaliana and to characterize their roles in supporting the parasitism of Heterodera schachtii. By selecting genes that were most strongly upregulated in response to cyst nematode infection, we identified HIPP27 (HEAVY METAL-ASSOCIATED ISOPRENYLATED PLANT PROTEIN 27) as a host susceptibility factor required for beet cyst nematode infection and development. Detailed expression analysis revealed that HIPP27 is a cytoplasmic protein and that HIPP27 is strongly expressed in leaves, young roots and nematode-induced syncytia. Loss-of-function Arabidopsis hipp27 mutants exhibited severely reduced susceptibility to H. schachtii and abnormal starch accumulation in syncytial and peridermal plastids. Our results suggest that HIPP27 is a susceptibility gene in Arabidopsis whose loss of function reduces plant susceptibility to cyst nematode infection without increasing the susceptibility to other pathogens or negatively affecting the plant phenotype.},
	language = {en},
	number = {8},
	urldate = {2024-08-30},
	journal = {Molecular Plant Pathology},
	author = {Radakovic, Zoran S. and Anjam, Muhammad Shahzad and Escobar, Elizabeth and Chopra, Divykriti and Cabrera, Javier and Silva, Ana Cláudia and Escobar, Carolina and Sobczak, Miroslaw and Grundler, Florian M. W. and Siddique, Shahid},
	year = {2018},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/mpp.12668},
	keywords = {HIPP27, Heterodera schachtii, cyst nematode, plant-parasitic nematodes, starch, susceptibility gene, syncytium},
	pages = {1917--1928},
}

Sedentary plant-parasitic cyst nematodes are obligate biotrophs that infect the roots of their host plant. Their parasitism is based on the modification of root cells to form a hypermetabolic syncytium from which the nematodes draw their nutrients. The aim of this study was to identify nematode susceptibility genes in Arabidopsis thaliana and to characterize their roles in supporting the parasitism of Heterodera schachtii. By selecting genes that were most strongly upregulated in response to cyst nematode infection, we identified HIPP27 (HEAVY METAL-ASSOCIATED ISOPRENYLATED PLANT PROTEIN 27) as a host susceptibility factor required for beet cyst nematode infection and development. Detailed expression analysis revealed that HIPP27 is a cytoplasmic protein and that HIPP27 is strongly expressed in leaves, young roots and nematode-induced syncytia. Loss-of-function Arabidopsis hipp27 mutants exhibited severely reduced susceptibility to H. schachtii and abnormal starch accumulation in syncytial and peridermal plastids. Our results suggest that HIPP27 is a susceptibility gene in Arabidopsis whose loss of function reduces plant susceptibility to cyst nematode infection without increasing the susceptibility to other pathogens or negatively affecting the plant phenotype.

@article{anwer_genome-wide_2018,
	title = {Genome-wide association study uncovers a novel {QTL} allele of {AtS40}-3 that affects the sex ratio of cyst nematodes in {Arabidopsis}},
	volume = {69},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/ery019},
	doi = {10.1093/jxb/ery019},
	abstract = {Plant-parasitic cyst nematodes are obligate sedentary parasites that infect the roots of a broad range of host plants. Cyst nematodes are sexually dimorphic, but differentiation into male or female is strongly influenced by interactions with the host environment. Female populations typically predominate under favorable conditions, whereas male populations predominate under adverse conditions. Here, we performed a genome-wide association study (GWAS) in an Arabidopsis diversity panel to identify host loci underlying variation in susceptibility to cyst nematode infection. Three different susceptibility parameters were examined, with the aim of providing insights into the infection process, the number of females and males present in the infected plant, and the female-to-male sex ratio. GWAS results suggested that variation in sex ratio is associated with a novel quantitative trait locus allele on chromosome 4. Subsequent candidate genes and functional analyses revealed that a senescence-associated transcription factor, AtS40-3, and PPR may act in combination to influence nematode sex ratio. A detailed molecular characterization revealed that variation in nematode sex ratio was due to the disturbed common promoter of AtS40-3 and PPR genes. Additionally, single nucleotide polymorphisms in the coding sequence of AtS40-3 might contribute to the natural variation in nematode sex ratio.},
	number = {7},
	urldate = {2024-08-30},
	journal = {Journal of Experimental Botany},
	author = {Anwer, Muhammad Arslan and Anjam, Muhammad Shahzad and Shah, Syed Jehangir and Hasan, M Shamim and Naz, Ali A and Grundler, Florian M W and Siddique, Shahid},
	month = mar,
	year = {2018},
	pages = {1805--1814},
}

Plant-parasitic cyst nematodes are obligate sedentary parasites that infect the roots of a broad range of host plants. Cyst nematodes are sexually dimorphic, but differentiation into male or female is strongly influenced by interactions with the host environment. Female populations typically predominate under favorable conditions, whereas male populations predominate under adverse conditions. Here, we performed a genome-wide association study (GWAS) in an Arabidopsis diversity panel to identify host loci underlying variation in susceptibility to cyst nematode infection. Three different susceptibility parameters were examined, with the aim of providing insights into the infection process, the number of females and males present in the infected plant, and the female-to-male sex ratio. GWAS results suggested that variation in sex ratio is associated with a novel quantitative trait locus allele on chromosome 4. Subsequent candidate genes and functional analyses revealed that a senescence-associated transcription factor, AtS40-3, and PPR may act in combination to influence nematode sex ratio. A detailed molecular characterization revealed that variation in nematode sex ratio was due to the disturbed common promoter of AtS40-3 and PPR genes. Additionally, single nucleotide polymorphisms in the coding sequence of AtS40-3 might contribute to the natural variation in nematode sex ratio.

@article{ali_signal_2018,
	title = {Signal {Transduction} in {Plant}–{Nematode} {Interactions}},
	volume = {19},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {1422-0067},
	url = {https://www.mdpi.com/1422-0067/19/6/1648},
	doi = {10.3390/ijms19061648},
	abstract = {To successfully invade and infect their host plants, plant parasitic nematodes (PPNs) need to evolve molecular mechanisms to overcome the defense responses from the plants. Nematode-associated molecular patterns (NAMPs), including ascarosides and certain proteins, while instrumental in enabling the infection, can be perceived by the host plants, which then initiate a signaling cascade leading to the induction of basal defense responses. To combat host resistance, some nematodes can inject effectors into the cells of susceptible hosts to reprogram the basal resistance signaling and also modulate the hosts’ gene expression patterns to facilitate the establishment of nematode feeding sites (NFSs). In this review, we summarized all the known signaling pathways involved in plant–nematode interactions. Specifically, we placed particular focus on the effector proteins from PPNs that mimic the signaling of the defense responses in host plants. Furthermore, we gave an updated overview of the regulation by PPNs of different host defense pathways such as salicylic acid (SA)/jasmonic acid (JA), auxin, and cytokinin and reactive oxygen species (ROS) signaling to facilitate their parasitic successes in plants. This review will enhance the understanding of the molecular signaling pathways involved in both compatible and incompatible plant–nematode interactions.},
	language = {en},
	number = {6},
	urldate = {2024-08-30},
	journal = {International Journal of Molecular Sciences},
	publisher = {Multidisciplinary Digital Publishing Institute},
	author = {Ali, Muhammad Amjad and Anjam, Muhammad Shahzad and Nawaz, Muhammad Amjad and Lam, Hon-Ming and Chung, Gyuhwa},
	month = jun,
	year = {2018},
	note = {Number: 6},
	keywords = {NAMP, NAMP-triggered immunity, NTI, PPN, nematode effector protein, nematode-associated molecular pattern, plant defense signaling pathway, plant parasitic nematode},
	pages = {1648},
}

To successfully invade and infect their host plants, plant parasitic nematodes (PPNs) need to evolve molecular mechanisms to overcome the defense responses from the plants. Nematode-associated molecular patterns (NAMPs), including ascarosides and certain proteins, while instrumental in enabling the infection, can be perceived by the host plants, which then initiate a signaling cascade leading to the induction of basal defense responses. To combat host resistance, some nematodes can inject effectors into the cells of susceptible hosts to reprogram the basal resistance signaling and also modulate the hosts’ gene expression patterns to facilitate the establishment of nematode feeding sites (NFSs). In this review, we summarized all the known signaling pathways involved in plant–nematode interactions. Specifically, we placed particular focus on the effector proteins from PPNs that mimic the signaling of the defense responses in host plants. Furthermore, we gave an updated overview of the regulation by PPNs of different host defense pathways such as salicylic acid (SA)/jasmonic acid (JA), auxin, and cytokinin and reactive oxygen species (ROS) signaling to facilitate their parasitic successes in plants. This review will enhance the understanding of the molecular signaling pathways involved in both compatible and incompatible plant–nematode interactions.

@article{shah_damage-associated_2017,
	title = {Damage-associated responses of the host contribute to defence against cyst nematodes but not root-knot nematodes},
	volume = {68},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erx374},
	doi = {10.1093/jxb/erx374},
	abstract = {When nematodes invade and subsequently migrate within plant roots, they generate cell wall fragments (in the form of oligogalacturonides; OGs) that can act as damage-associated molecular patterns and activate host defence responses. However, the molecular mechanisms mediating damage responses in plant–nematode interactions remain unexplored. Here, we characterized the role of a group of cell wall receptor proteins in Arabidopsis, designated as polygalacturonase-inhibiting proteins (PGIPs), during infection with the cyst nematode Heterodera schachtii and the root-knot nematode Meloidogyne incognita. PGIPs are encoded by a family of two genes in Arabidopsis, and are involved in the formation of active OG elicitors. Our results show that PGIP gene expression is strongly induced in response to cyst nematode invasion of roots. Analyses of loss-of-function mutants and overexpression lines revealed that PGIP1 expression attenuates infection of host roots by cyst nematodes, but not root-knot nematodes. The PGIP1-mediated attenuation of cyst nematode infection involves the activation of plant camalexin and indole-glucosinolate pathways. These combined results provide new insights into the molecular mechanisms underlying plant damage perception and response pathways during infection by cyst and root-knot nematodes, and establishes the function of PGIP in plant resistance to cyst nematodes.},
	number = {21-22},
	urldate = {2024-08-30},
	journal = {Journal of Experimental Botany},
	author = {Shah, Syed Jehangir and Anjam, Muhammad Shahzad and Mendy, Badou and Anwer, Muhammad Arslan and Habash, Samer S and Lozano-Torres, Jose L and Grundler, Florian M W and Siddique, Shahid},
	month = dec,
	year = {2017},
	pages = {5949--5960},
}

When nematodes invade and subsequently migrate within plant roots, they generate cell wall fragments (in the form of oligogalacturonides; OGs) that can act as damage-associated molecular patterns and activate host defence responses. However, the molecular mechanisms mediating damage responses in plant–nematode interactions remain unexplored. Here, we characterized the role of a group of cell wall receptor proteins in Arabidopsis, designated as polygalacturonase-inhibiting proteins (PGIPs), during infection with the cyst nematode Heterodera schachtii and the root-knot nematode Meloidogyne incognita. PGIPs are encoded by a family of two genes in Arabidopsis, and are involved in the formation of active OG elicitors. Our results show that PGIP gene expression is strongly induced in response to cyst nematode invasion of roots. Analyses of loss-of-function mutants and overexpression lines revealed that PGIP1 expression attenuates infection of host roots by cyst nematodes, but not root-knot nematodes. The PGIP1-mediated attenuation of cyst nematode infection involves the activation of plant camalexin and indole-glucosinolate pathways. These combined results provide new insights into the molecular mechanisms underlying plant damage perception and response pathways during infection by cyst and root-knot nematodes, and establishes the function of PGIP in plant resistance to cyst nematodes.

@article{anjam_improved_2016,
	title = {An improved procedure for isolation of high-quality {RNA} from nematode-infected {Arabidopsis} roots through laser capture microdissection},
	volume = {12},
	issn = {1746-4811},
	url = {https://doi.org/10.1186/s13007-016-0123-9},
	doi = {10.1186/s13007-016-0123-9},
	abstract = {Cyst nematodes are biotrophs that form specialized feeding structures in the roots of host plants, which consist of a syncytial fusion of hypertrophied cells. The formation of syncytium is accompanied by profound transcriptional changes and active metabolism in infected tissues. The challenge in gene expression studies for syncytium has always been the isolation of pure syncytial material and subsequent extraction of intact RNA. Root fragments containing syncytium had been used for microarray analyses. However, the inclusion of neighbouring cells dilutes the syncytium-specific mRNA population. Micro-sectioning coupled with laser capture microdissection (LCM) offers an opportunity for the isolation of feeding sites from heterogeneous cell populations. But recovery of intact RNA from syncytium dissected by LCM is complicated due to extended steps of fixation, tissue preparation, embedding and sectioning.},
	number = {1},
	urldate = {2024-08-30},
	journal = {Plant Methods},
	author = {Anjam, Muhammad Shahzad and Ludwig, Yvonne and Hochholdinger, Frank and Miyaura, Chisato and Inada, Masaki and Siddique, Shahid and Grundler, Florian M. W.},
	month = apr,
	year = {2016},
	keywords = {Arabidopsis, Cyst nematode, LCM, Nematode, RNA degradation, Root, Syncytium},
	pages = {25},
}

Cyst nematodes are biotrophs that form specialized feeding structures in the roots of host plants, which consist of a syncytial fusion of hypertrophied cells. The formation of syncytium is accompanied by profound transcriptional changes and active metabolism in infected tissues. The challenge in gene expression studies for syncytium has always been the isolation of pure syncytial material and subsequent extraction of intact RNA. Root fragments containing syncytium had been used for microarray analyses. However, the inclusion of neighbouring cells dilutes the syncytium-specific mRNA population. Micro-sectioning coupled with laser capture microdissection (LCM) offers an opportunity for the isolation of feeding sites from heterogeneous cell populations. But recovery of intact RNA from syncytium dissected by LCM is complicated due to extended steps of fixation, tissue preparation, embedding and sectioning.

@incollection{manzoor_avenues_2016,
	title = {Avenues for improving drought tolerance in crops by {ABA} regulation},
	copyright = {© 2016 John Wiley \& Sons, Ltd.},
	isbn = {978-1-119-05445-0},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/9781119054450.ch13},
	doi = {10.1002/9781119054450.ch13},
	abstract = {Crop productivity is greatly reduced due to abiotic stresses including drought stress. Naturally occurring drought stress tolerant plants have evolved some adaptations to cope with drought stress. Based on drought adaptive responses in wild or crop plants, plant scientists are pursuing efforts to develop crop tolerance against drought stress using heritable traits that contribute in drought tolerance through conventional or advanced molecular techniques. Among these drought tolerance traits, organic compatible solutes, antioxidant compounds, and plant growth regulators are of great significance. Among various plant growth regulators, abscisic acid (ABA) is known to regulate environmental stress responses in plants by affecting transpirational water loss, stomatal closure, photosynthesis, water use efficiency, seed development and maturation, leaf senescence and cell membrane protection, and so on. The degree of biosynthesis and accumulation of ABA in a crop cultivar is a possible indicator of drought tolerance. Drought stress-regulated ABA biosynthesis depends on a key enzyme, 9-cis-epoxycarotenoid dioxygenase (NCED) involved in ABA biosynthesis. NCED3 and/or its corresponding orthologs could be valuable targets for improving drought tolerance in crops. In all ABA-dependent physiological and developmental processes, regulation of ABA signaling is central to develop drought tolerance in plants. A number of drought tolerance related functional and regulatory genes that are regulated by ABA have been discovered, of which bZIP transcription factors (TFs), ABI5, AREB/ABFs, SnRK2-AREB/ABF, and WRKY are of key importance. However, impact of these genes in developing drought tolerance is confounded in some cases because drought tolerance mechanism is very complex and varies with plant developmental stage. In addition, an ABA-independent pathway for drought tolerance also exists in plants, which causes further complexity in understanding the mechanisms of drought tolerance. Finding missing links in sensing and response components of ABA signaling cascades using a wide range of high-throughput analytical techniques for measuring metabolites, proteins, and transcripts in plant tissues will pave new avenues for studying stress resistance in crops.},
	language = {en},
	urldate = {2024-08-30},
	booktitle = {Water {Stress} and {Crop} {Plants}},
	publisher = {John Wiley \& Sons, Ltd},
	author = {Manzoor, Hamid and Athar, Habib-ur-Rehman and Rasul, Sumaira and Kanwal, Tehseen and Anjam, Muhammad Shahzad and Qureshi, Muhammad Kamran and Bashir, Nahidah and Zafar, Zafar Ullah and Ali, Muhammad and Ashraf, Muhammad},
	year = {2016},
	note = {Section: 13
\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/9781119054450.ch13},
	keywords = {NCED3, abscisic acid, crop improvement, hormones, osmotic stress, photosynthesis, signal transduction},
	pages = {177--193},
}

Crop productivity is greatly reduced due to abiotic stresses including drought stress. Naturally occurring drought stress tolerant plants have evolved some adaptations to cope with drought stress. Based on drought adaptive responses in wild or crop plants, plant scientists are pursuing efforts to develop crop tolerance against drought stress using heritable traits that contribute in drought tolerance through conventional or advanced molecular techniques. Among these drought tolerance traits, organic compatible solutes, antioxidant compounds, and plant growth regulators are of great significance. Among various plant growth regulators, abscisic acid (ABA) is known to regulate environmental stress responses in plants by affecting transpirational water loss, stomatal closure, photosynthesis, water use efficiency, seed development and maturation, leaf senescence and cell membrane protection, and so on. The degree of biosynthesis and accumulation of ABA in a crop cultivar is a possible indicator of drought tolerance. Drought stress-regulated ABA biosynthesis depends on a key enzyme, 9-cis-epoxycarotenoid dioxygenase (NCED) involved in ABA biosynthesis. NCED3 and/or its corresponding orthologs could be valuable targets for improving drought tolerance in crops. In all ABA-dependent physiological and developmental processes, regulation of ABA signaling is central to develop drought tolerance in plants. A number of drought tolerance related functional and regulatory genes that are regulated by ABA have been discovered, of which bZIP transcription factors (TFs), ABI5, AREB/ABFs, SnRK2-AREB/ABF, and WRKY are of key importance. However, impact of these genes in developing drought tolerance is confounded in some cases because drought tolerance mechanism is very complex and varies with plant developmental stage. In addition, an ABA-independent pathway for drought tolerance also exists in plants, which causes further complexity in understanding the mechanisms of drought tolerance. Finding missing links in sensing and response components of ABA signaling cascades using a wide range of high-throughput analytical techniques for measuring metabolites, proteins, and transcripts in plant tissues will pave new avenues for studying stress resistance in crops.

@article{siddique_parasitic_2015,
	title = {A parasitic nematode releases cytokinin that controls cell division and orchestrates feeding site formation in host plants},
	volume = {112},
	url = {https://www.pnas.org/doi/10.1073/pnas.1503657112},
	doi = {10.1073/pnas.1503657112},
	abstract = {Sedentary plant-parasitic cyst nematodes are biotrophs that cause significant losses in agriculture. Parasitism is based on modifications of host root cells that lead to the formation of a hypermetabolic feeding site (a syncytium) from which nematodes withdraw nutrients. The host cell cycle is activated in an initial cell selected by the nematode for feeding, followed by activation of neighboring cells and subsequent expansion of feeding site through fusion of hundreds of cells. It is generally assumed that nematodes manipulate production and signaling of the plant hormone cytokinin to activate cell division. In fact, nematodes have been shown to produce cytokinin in vitro; however, whether the hormone is secreted into host plants and plays a role in parasitism remained unknown. Here, we analyzed the spatiotemporal activation of cytokinin signaling during interaction between the cyst nematode, Heterodera schachtii, and Arabidopsis using cytokinin-responsive promoter:reporter lines. Our results showed that cytokinin signaling is activated not only in the syncytium but also in neighboring cells to be incorporated into syncytium. An analysis of nematode infection on mutants that are deficient in cytokinin or cytokinin signaling revealed a significant decrease in susceptibility of these plants to nematodes. Further, we identified a cytokinin-synthesizing isopentenyltransferase gene in H. schachtii and show that silencing of this gene in nematodes leads to a significant decrease in virulence due to a reduced expansion of feeding sites. Our findings demonstrate the ability of a plant-parasitic nematode to synthesize a functional plant hormone to manipulate the host system and establish a long-term parasitic interaction.},
	number = {41},
	urldate = {2024-08-30},
	journal = {Proceedings of the National Academy of Sciences},
	publisher = {Proceedings of the National Academy of Sciences},
	author = {Siddique, Shahid and Radakovic, Zoran S. and De La Torre, Carola M. and Chronis, Demosthenis and Novák, Ondřej and Ramireddy, Eswarayya and Holbein, Julia and Matera, Christiane and Hütten, Marion and Gutbrod, Philipp and Anjam, Muhammad Shahzad and Rozanska, Elzbieta and Habash, Samer and Elashry, Abdelnaser and Sobczak, Miroslaw and Kakimoto, Tatsuo and Strnad, Miroslav and Schmülling, Thomas and Mitchum, Melissa G. and Grundler, Florian M. W.},
	month = oct,
	year = {2015},
	pages = {12669--12674},
}

Sedentary plant-parasitic cyst nematodes are biotrophs that cause significant losses in agriculture. Parasitism is based on modifications of host root cells that lead to the formation of a hypermetabolic feeding site (a syncytium) from which nematodes withdraw nutrients. The host cell cycle is activated in an initial cell selected by the nematode for feeding, followed by activation of neighboring cells and subsequent expansion of feeding site through fusion of hundreds of cells. It is generally assumed that nematodes manipulate production and signaling of the plant hormone cytokinin to activate cell division. In fact, nematodes have been shown to produce cytokinin in vitro; however, whether the hormone is secreted into host plants and plays a role in parasitism remained unknown. Here, we analyzed the spatiotemporal activation of cytokinin signaling during interaction between the cyst nematode, Heterodera schachtii, and Arabidopsis using cytokinin-responsive promoter:reporter lines. Our results showed that cytokinin signaling is activated not only in the syncytium but also in neighboring cells to be incorporated into syncytium. An analysis of nematode infection on mutants that are deficient in cytokinin or cytokinin signaling revealed a significant decrease in susceptibility of these plants to nematodes. Further, we identified a cytokinin-synthesizing isopentenyltransferase gene in H. schachtii and show that silencing of this gene in nematodes leads to a significant decrease in virulence due to a reduced expansion of feeding sites. Our findings demonstrate the ability of a plant-parasitic nematode to synthesize a functional plant hormone to manipulate the host system and establish a long-term parasitic interaction.

@article{shaikh_frequency_2010,
	title = {Frequency distribution of \textit{{GSTM1}} and \textit{{GSTT1}} null allele in {Pakistani} population and risk of disease incidence},
	volume = {30},
	issn = {1382-6689},
	url = {https://www.sciencedirect.com/science/article/pii/S1382668910000852},
	doi = {10.1016/j.etap.2010.04.002},
	abstract = {Glutathione-S-transferases, GSTM1 and GSTT1 play a significant role in detoxification and bioactivation of a broad range of xenobiotic compounds known to be mutagenic and/or carcinogenic. Deletion polymorphisms of these glutathione transferases (GSTM1 and GSTT1) predispose individuals to environmental carcinogenic compounds. Although a number of studies have shown the relationship between GSTM1 and/or GSTT1 deletion polymorphism and different cancers, these findings cannot be extrapolated to other populations due to intra- and inter-ethnic variability. In order to assess the impact of differential ethnicity on the occurrence of different cancers in local population due to GSTM1, or GSTT1 deletion polymorphism, 111 healthy male and female individuals of different age groups from Southern Punjab, Pakistan were genotyped using a multiplex polymerase chain reaction. From the results it is obvious that null alleles of GSTM1 and GSTT1 genes were found in 45\% and 23\% individuals, respectively. In 5\% of individuals’ simultaneous deletion of both GSTM1 and GSTT1 genes were observed. Frequency of GSTM1 null allele is in concordance with those documented for Chinese, Caucasians, Mongolian, and Japanese populations. However, a significantly higher frequency for GSTT1 null was reported in Chinese and Japanese population as compared to Pakistani population. It is the first ever report on frequency of GSTM1 and GSTT1 null allele in Pakistani population which demonstrate the impact of ethnicity and provide basis for future epidemiological and clinical studies.},
	number = {1},
	urldate = {2024-08-30},
	journal = {Environmental Toxicology and Pharmacology},
	author = {Shaikh, Rehan Sadiq and Amir, Muhammad and Masood, Ahmed Ijaz and Sohail, Asma and Athar, Habib-ur-Rehman and Siraj, Sami and Ali, Muhammad and Anjam, Muhammad Shahzad},
	month = jul,
	year = {2010},
	keywords = {Genetic susceptibility, Inter-ethnic variability, Null allele polymorphism, Xenobiotic metabolizing enzymes},
	pages = {76--79},
}

Glutathione-S-transferases, GSTM1 and GSTT1 play a significant role in detoxification and bioactivation of a broad range of xenobiotic compounds known to be mutagenic and/or carcinogenic. Deletion polymorphisms of these glutathione transferases (GSTM1 and GSTT1) predispose individuals to environmental carcinogenic compounds. Although a number of studies have shown the relationship between GSTM1 and/or GSTT1 deletion polymorphism and different cancers, these findings cannot be extrapolated to other populations due to intra- and inter-ethnic variability. In order to assess the impact of differential ethnicity on the occurrence of different cancers in local population due to GSTM1, or GSTT1 deletion polymorphism, 111 healthy male and female individuals of different age groups from Southern Punjab, Pakistan were genotyped using a multiplex polymerase chain reaction. From the results it is obvious that null alleles of GSTM1 and GSTT1 genes were found in 45% and 23% individuals, respectively. In 5% of individuals’ simultaneous deletion of both GSTM1 and GSTT1 genes were observed. Frequency of GSTM1 null allele is in concordance with those documented for Chinese, Caucasians, Mongolian, and Japanese populations. However, a significantly higher frequency for GSTT1 null was reported in Chinese and Japanese population as compared to Pakistani population. It is the first ever report on frequency of GSTM1 and GSTT1 null allele in Pakistani population which demonstrate the impact of ethnicity and provide basis for future epidemiological and clinical studies.

@misc{minhas_r_minhas_2008,
	title = {Minhas: {Genetics} of some fiber quality traits among... - {Google} {Scholar}},
	url = {https://scholar.google.com/scholar_lookup?&title=Genetics%20of%20some%20fiber%20quality%20traits%20among%20intraspecific%20crosses%20of%20American%20cotton%20%28Gossypium%20hirsutum%20L.%29&journal=Int%20J%20Agric%20Biol&volume=10&issue=2&pages=196-200&publication_year=2008&author=Minhas%2CR&author=Khan%2CIA&author=Anjam%2CMS&author=Ali%2CK},
	abstract = {Five American cotton (Gossypium hirsutum L.) varieties namely Coker-4601, MNH-552, S-14, Stoneville and Allepo-41 were crossed in a complete diallel fashion and evaluated in randomized complete block design. Gene action and combining ability effects were estimated for the fiber quality its fineness, staple length, uniformity ratio and strength. Fiber fineness, staple length and fiber strength were found to be controlled by additive type of gene action with partial dominance while fiber uniformity ratio with over dominance type of gene action. For fiber fineness and staple length genotype Coker-4601 was a good general combiner whereas S-14 and Stoneville were good combiner for fiber uniformity ratio and its strength. The cross combinations, Coker-4601 X Stoneville showed better SCA for staple length and fiber strength while Coker-4601 X Allepo-41 and Coker-4601 X S-14 showed good SCA for fiber fineness and fiber uniformity ratio.},
	urldate = {2024-08-30},
	author = {{Minhas R} and {Khan IA} and {Anjam MS} and {Ali K}},
	year = {2008},
}

Five American cotton (Gossypium hirsutum L.) varieties namely Coker-4601, MNH-552, S-14, Stoneville and Allepo-41 were crossed in a complete diallel fashion and evaluated in randomized complete block design. Gene action and combining ability effects were estimated for the fiber quality its fineness, staple length, uniformity ratio and strength. Fiber fineness, staple length and fiber strength were found to be controlled by additive type of gene action with partial dominance while fiber uniformity ratio with over dominance type of gene action. For fiber fineness and staple length genotype Coker-4601 was a good general combiner whereas S-14 and Stoneville were good combiner for fiber uniformity ratio and its strength. The cross combinations, Coker-4601 X Stoneville showed better SCA for staple length and fiber strength while Coker-4601 X Allepo-41 and Coker-4601 X S-14 showed good SCA for fiber fineness and fiber uniformity ratio.

@article{anjam_evaluation_2005,
	title = {Evaluation and correlation of economically important traits in exotic germplasm of lentil},
	volume = {7},
	number = {6},
	urldate = {2024-08-30},
	journal = {Int. J. Agric. Biol},
	author = {Anjam, MUHAMMAD SHAHZAD and Ali, ASGHAR and Iqbal, Sh M. and Haqqani, ABDUL MAJEED},
	year = {2005},
	keywords = {⛔ No DOI found},
	pages = {959--961},
}

@article{anjam_evaluation_2005,
	title = {Evaluation of lentil genotypes for resistance to pea seed-borne mosaic virus. {Int} {J} {Agric} {Biol} 7:148-149},
	volume = {7},
	shorttitle = {Evaluation of lentil genotypes for resistance to pea seed-borne mosaic virus. {Int} {J} {Agric} {Biol} 7},
	abstract = {Sixty-four lentil genotypes obtained from International Center for Agricultural Research in Dry Areas (ICARDA), Syria were evaluated against pea seed-borne mosaic virus (PSbMV). There was a wide range of variability in disease reaction among the genotypes. Most of the genotypes were found tolerant to this disease. Out of 64 lines, 21 were found resistant, 28 tolerant, and 15 susceptible. This study reports some additional sources of resistance in world collection of lentil germplasm against PSbMV which may be useful for breeding programmes.},
	journal = {International Journal of Agriculture and Biology},
	author = {Anjam, Muhammad and Iqbal, S.M. and Ali, Asghar and Tahir, Muhammad},
	month = jan,
	year = {2005},
	keywords = {⛔ No DOI found},
	pages = {148--149},
}

Sixty-four lentil genotypes obtained from International Center for Agricultural Research in Dry Areas (ICARDA), Syria were evaluated against pea seed-borne mosaic virus (PSbMV). There was a wide range of variability in disease reaction among the genotypes. Most of the genotypes were found tolerant to this disease. Out of 64 lines, 21 were found resistant, 28 tolerant, and 15 susceptible. This study reports some additional sources of resistance in world collection of lentil germplasm against PSbMV which may be useful for breeding programmes.