Biology subjects

Ashraf, A.

Publications and source records attributed to Ashraf, A..

12 recordsLinked to original sources

bioRxiv2026

Harmala alkaloids regulate cell division planes in plants

Plants produce a vast diversity of specialized metabolites that function as chemical defenses against herbivores, pathogens, and competing plants. Many of these compounds also act as powerful tools for biological discovery, revealing fundamental cellular mechanisms through their effects on living systems. Among these metabolites, the harmala alkaloids from Peganum harmala (Syrian rue) possess cross-kingdom biological effects, including medicinal and neuroactive activity in humans, and allelopathic, growth-inhibiting effects on other plant species. However, the cellular processes in plants that are targeted by the harmala alkaloids are unknown. Here, we investigated the effects of the harmala alkaloids on plant growth and cell division using Arabidopsis thaliana as a model system. Of the harmala alkaloids, harmaline was identified as the most potent compound for root growth inhibition. Quantitative live cell imaging demonstrated that harmaline exposure causes progressive defects in cell division orientation and root cell morphology in a temporal manner. Furthermore, we identified harmaline-mediated phragmoplast orientation and morphology defects, pointing to a potential target related to phragmoplast guidance proteins. These findings position harmaline as a promising chemical probe for investigating the mechanisms that govern division plane positioning in plant cells and highlight a putative pathway by which harmala alkaloids exert allelopathic effects in competing plants. One sentence summaryHarmala alkaloids regulate cell division plane as an allelopathic mechanism

plant biology↗

bioRxiv2026

Leaves in Transition: Single nuclei RNA sequencing provides insights into sorghums juvenile and adult phases

The transition from juvenile to adult phase (JA) is a key developmental process in plants, driven by conserved pathways that shape growth and stress responses. In monocots such as sorghum, this transition influences traits linked to environmental resilience, yet the regulation of micro-anatomical features such as trichomes and bulliform cells remains poorly understood. Here, we use single-nucleus RNA sequencing (snRNA-seq) to generate high-resolution gene expression maps of juvenile and adult sorghum leaves. Contrary to the traditional developmental model, we find that trichomes are present in both juvenile and adult leaves, with stage-dependent differences in gene expression. We also observe that bulliform cells, typically considered adult-specific, are present in juvenile leaves. At the transcriptomic level, cell populations cluster more strongly by developmental stage than by cell type, with juvenile cells grouping with other juvenile cells and adult cells with adult counterparts, indicating a dominant effect of developmental state on gene expression. In addition, we identify enrichment of dhurrin biosynthetic genes in trichome-associated cells as well as elevated expression of aquaporin genes in these cells, pointing to a potential role for trichomes in coordinating defense and water-related processes. Together, these findings refine current models of sorghum development and suggest that key epidermal cells and their associated functions may be established earlier than previously known. Collectively, this study provides a single nucleus resolved framework for understanding how developmental stage shapes gene expression in sorghum leaves.

plant biology↗

bioRxiv2026

Quantitative live cell imaging of nuclear shape and chromatin dynamics during development and environmental stress in Arabidopsis thaliana

The nucleus is the characteristic organelle for eukaryotic organisms. Unlike the classic textbook view of static two-dimensional nuclei, nuclear shape is dynamic inside the live cell. The alteration or deformed nuclear shape is the hallmark of cancer in animal cells and environmental stress in plants. The nuclear envelope proteins interact with chromatin to regulate gene expression. Unfortunately, we have limited knowledge about the impact of abiotic stress on nuclear shape, movement, and chromatin dynamics. To circumvent this issue, we are utilizing a dual fluorescently tagged marker lines - nuclear envelope protein and chromatin - to perform live cell imaging in the model plant Arabidopsis thaliana root. The live cell imaging was performed in control and salt-stressed conditions. We utilized these captured movies to analyze through open-source image processing software Fiji/ImageJ with the help of the TrackMate plugin. Using this method, we have demonstrated that chromatin velocity is decreased in salt-treated conditions. This method will be widely applied to quantitative live cell imaging of nuclear shape and chromatin dynamics during plant development and environmental stress. SummaryThis process aims to simultaneously record nucleus and chromatin dynamics in Arabidopsis thaliana roots and investigate changes in these dynamics in response to developmental and environmental cues.

plant biology↗

bioRxiv2026

Simultaneous triple staining for detecting cell-type specific spatio-temporal distribution of cell wall materials in monocot roots

O_LIAnatomical and histochemical imaging of grass root systems relies on tissue sectioning and cell wall staining dyes because molecular reporter lines are limited for most organisms. C_LIO_LIDistinct staining dyes require variable incubation time and concentration across different tissues and organisms. As a result, staining with multiple dyes becomes time consuming or challenging. Here, we report a rapid method to perform simultaneous triple staining on a glass slide. The entire protocol requires [~]4 hours and a smaller volume of stain than traditional methods. C_LIO_LIWe tested this method using the roots of two economically important crops, Triticum aestivum (wheat) and Zea mays (maize), as proof of concept. We have also demonstrated the presence of exodermis in wheat roots. Additionally, we identified the formation of polar lignin caps in maize exodermis using our simultaneous triple staining method. C_LIO_LIThis method empowers a quantitative approach to cell biology by elucidating cell-type specific spatio-temporal distribution of cell wall materials in monocot root systems. C_LI

plant biology↗

bioRxiv2026

Toxic metals increase root hair density by reducing epidermal cell length

Root hair cells, which are instrumental in water and nutrient uptake, grow polarly from the epidermal cell layer of the root. Furthermore, plants growing in challenging climates and complex soil environments acclimatize their root hair phenotypes, either by altering root hair length or density. Toxic metal stress is one of the major environmental stresses faced by plant roots. In this study, we demonstrate that toxic metals, such as chromium and arsenite, increase root hair density as an adaptive response. Using the model plant Arabidopsis thaliana and other crops plants, like Zea mays and Triticum aestivum, we further discovered that increased root hair density is caused by shorter epidermal cell length rather than alteration of epidermal cell fate. This study highlights the adaptive cellular and anatomical features of roots during toxic metal stress in evolutionary diverse plant species.

plant biology↗

bioRxiv2025

The nucleus follows an internal cellular scale during polarized root hair cell development

The root hair cell is a product of asymmetric cell division, which grows in a polar manner, and thus is an attractive model cell type from a cellular biology aspect. Beyond the fundamental cell biology context, the root hair is involved in water and nutrient acquisition, making it important for agronomic applications. Nuclear positioning in the cell is crucial during root hair development. Often, textbooks demonstrate illustrations of the nucleus located at a fixed position from the tip of a root hair or at the very end of a root hair. The fundamental question is whether the nucleus follows a cellular scale during polarized growth. Maintaining the scale is a rudimentary biological process during development at the organismal and cellular levels. In this study, we altered root hairs through hormonal, nutrient, and environmental factors to decipher the cellular scale (no scale, universal scale, or internal scale) maintained by the nucleus. We utilized the live cell imaging combined with a quantitative cell biology approach and, surprisingly discovered that the nucleus always follows an internal scale in the root hair cell. This finding dramatically shifted our view about the nuclear position in a polarized cell and will have a potential to test across the tree of life. Altogether, understanding the cellular scale involved with nucleus positioning will have broad implications. It encourages a reexamination of textbooks and reinforces the agricultural importance in a changing climate.

plant biology↗

bioRxiv2025

Cell cycle follows pause and play mechanism in environment stress recovery in diverse plant species

Changes to organismal growth induced by environmental stress are orchestrated at the cellular level. These periods of stress may be followed by recovery periods, when plants have the opportunity to return to normal growth conditions. However, the cell cycle mechanisms underlying recovery are poorly understood. We tested the cell cycle regulation in roots during control, stress, and recovery period for salt, osmotic, cold, and heat stresses using Arabidopsis thaliana, Brachypodium distachyon and Lolium multiflorum. During the salt and cold stress conditions, the cell cycle pauses at gap phase and is released from gap phase during stress recovery, which depends on CDKA;1 and ICK1. Cold stress and recovery, which specifically relies on cell division, follows a conserved "pause and play" mechanism of cell cycle.

plant biology↗

bioRxiv2024

Macrophage migration-dependent retraction fibers and migrasomes - a structural basis for spatiotemporal cytokine secretion.

Migrating cells leave behind trails of matrix-bound retraction fibers and migrasomes, but their cell-specific physiological functions are largely unknown. We comprehensively characterize retraction fibers and migrasomes of migrating macrophages in mouse and zebrafish in vitro and in vivo models. These structures share common and macrophage-centric components of tetraspanin enriched microdomains (TEMs) including tetraspanin 4 (TSPAN4), the integrin CD11b and the pTRAP, SCIMP; like TSPAN4, we show that SCIMP expression modulates retraction fiber and migrasome formation. In immune-activated migrating macrophages, rear-positioned recycling endosomes regulate the secretory trafficking of newly synthesized inflammatory cytokines into retraction fibers and migrasomes. Transmembrane TNF is delivered via SNARE-mediated carriers to the cell surface and to the surfaces of both retraction fibers and migrasomes, from where it can be released. Retraction fibers are thus newly identified here as cytokine secretion sites, and along with migrasomes they allow migrating macrophages to secrete more cytokine compared to stationary cells. Whereas cytokine secretion has been viewed as a process of ad hoc diffusion, instead, we reveal a new mechanism of migration-dependent, localized deposition and spatiotemporal release of bioactive cytokines from RFs and migrasomes. Cytokine deployment is thus organized in a constrained manner facilitating direct influence on local inflammatory responses.

cell biology↗

bioRxiv2024

Priming Epigenetic Landscape at Gene Promoters through Transcriptional Activation in Mammalian Germ Cells

In mammalian germ cells, a cycle of erasing and resetting epigenetic information is crucial for sex-specific gametogenesis and early embryogenesis. Specific chromatin states at promoters allow genes to be expressed at the appropriate time during germ cell development, however, the mechanism that establishes such characteristic chromatin states remains unclear. Here, we show that, in mouse male embryonic germ cells, promoters of developmental and housekeeping genes are selectively protected from de novo DNA methylation, coinciding with their transient upregulation and genome-wide erasure of H3K27me3. Importantly, a specific level of H3K4me3 density at the promoters serves as a potent probe that distinguishes between hypo- and hyper-DNA methylation states. Subsequent restoration of H3K27me3 contributes to establishing bivalent chromatin states that prime genes for activation at later developmental stages. These findings reveal a molecular framework shaping the epigenetic landscape at promoters with long-term effects beyond germ cell development.

genomics↗

bioRxiv2024

Monocytes Mobilized by Gut Neurons Remodel the Enteric Nervous System

The proper organization of the enteric nervous system (ENS) is critical for normal gastrointestinal (GI) physiology. Inflammatory bowel disease (IBD) dysregulates GI physiology, including bowel movements (motility), but in many IBD patients, GI motility disorders persist in remission through a poorly understood pathological process. Here we uncover that post-inflammatory GI dysmotility (PI-GID) stems from structural ENS remodeling driven by a combination of neuronal loss and neurogenesis. Enteric neurons respond to mucosal inflammation by upregulating CCL2 expression and facilitating the recruitment of CCR2+ monocytes into the neural myenteric plexus within the intestinal muscle. This is followed by the expansion of monocyte-derived macrophages and their migration into the myenteric ganglia and phagocytosis of neurons. However, excessive recruitment of monocytes results in disproportionate ENS remodeling and PI-GID. The expansion of inflammatory cells is known to promote tissue hypoxia. We find that enteric neurons become hypoxic upon colitis, but hypoxia-induced signaling via HIF1 initiates an adaptation program in enteric neurons to attenuate CCL2 expression and limit monocyte recruitment. We demonstrate that reinforcing HIF1 signaling in enteric neurons prevents PI-GID by reducing colitis-associated monocyte recruitment in the myenteric plexus and protecting against ENS remodeling. In summary, our findings unveil PI-GID pathogenesis and identify a regulatory axis for its prevention. One Sentence SummaryIntestinal mucosal inflammation engages enteric neurons in the inflammatory response leading to neurogenic recruitment of monocytes into the extra-mucosal myenteric plexus followed by pathological structural remodeling of the enteric nervous system by monocyte-derived macrophages.

immunology↗

bioRxiv2023

Stomatal closure in maize is mediated by subsidiary cells and the PAN2 receptor

Stomata are epidermal pores that facilitate plant gas exchange. Grasses have fast stomatal movements, likely due to their dumbbell-shaped guard cells and lateral subsidiary cells. Subsidiary cells reciprocally exchange water and ions with guard cells. However, the relative contribution of subsidiary cells during stomatal closure is unresolved. We compared stomatal gas exchange and stomatal aperture dynamics in wild type and pan1, pan2, and pan1;pan2 Zea mays (L.) (maize) mutants, which have varying percentages of aberrantly formed subsidiary cells. Stomata with 1 or 2 defective subsidiary cells cannot close properly, indicating that subsidiary cells are essential for stomatal function. Even though the percentage of aberrant stomata is similar in pan1 and pan2, pan2 showed a more severe defect in stomatal closure. In pan1, only stomata with abnormal subsidiary cells fail to close normally. In pan2, all stomata have stomatal closure defects, indicating that PAN2 has an additional role in stomatal closure. Maize Pan2 is orthologous to Arabidopsis GHR1, which is also required for stomatal closure. PAN2 acts downstream of Ca2+ in maize to promote stomatal closure. This is in contrast to GHR1, which acts upstream of Ca2+, and suggests the pathways could be differently wired.

plant biology↗

bioRxiv2023

In-silico Screening of Origanum vulgare Phytocompounds as Potential Drug Agents Against Vp35 Protein of the Ebola Virus

The leading cause of the Ebola virus outbreak during 2013-16 in Western Africa was a lack of targeted anti- viral drug choices, a fast rate of mutations and the unavailability of many of the structural proteins and annotations within its genome. The surroundings of the Ebola River in DR-Congo fail to get rid of this endemic, the reason behind this was believed to be its origin from non-human primates, which made its risk assessment and tracing difficult. The Vp35 is a multifunctional protein with innate immune antagonistic properties and is considered one of the most suitable drug targets within this virus. The main motive of this study is to discover a potential anti-viral drug against the Ebola virus by targeting the aforementioned protein with different phytocompounds of oregano that have the lowest binding energies and qualifies over different simulation parameters, so firstly, molecular docking was performed on its 28 compounds using PyRx to get the best complexes with minimum binding energies e.g., -8.9Kcal/mol. Ligands with the best docking scores were gone through Lipinskis rule of five for drug likeliness potential. For the drug affirmation, molecular dynamic simulation was also performed with the best two docked complexes using NAMD/VMD to find out their conformational stability through RMSD, RMSF, Rg, SASA and H-bond analyses. Current computer-generated prediction suggested that Ursolic acid and Oleanolic acid possess potential inhibitory effects against virus replication. Furthermore, paradigm shifts of usage of natural and herbal products for treating infectious diseases are being encouraged here, However, further wet-lab experiments and clinical trials are still needed to determine the robustness of these virtually tested phytocompounds against the Vp35 protein of the Ebola virus.

bioinformatics↗