Biology subjects

Saxena, P.

Publications and source records attributed to Saxena, P..

4 recordsLinked to original sources

bioRxiv2026

Combining 3D-multispectral and hyperspectral imaging to identify environmental stress treatments imposed during plant growth

Non-invasive, high-throughput phenotyping tools are needed that can identify environmental effects on plant structure and function to diagnose factors responsible for reduced growth in commercial and non-commercial settings. In this study, we explored whether the integration of 3D-multispectral (3D) and 2D-hyperspectral imaging (HSI), aided by machine learning (ML), could be used to identify environmental stress treatments imposed during plant growth. Controlled environment-grown Nicotiana Benthamiana plants were subjected to a range of abiotic treatments - including different growth irradiances, heat treatment and drought stress - with the treatments resulting in differences in shoot height, biomass, leaf area and spectral reflectance. ML models were trained to identify these treatments using morphological and spectral traits measured at 27, 29, 31, and 34 days after sowing (DAS). A 3D-multispectral scanner was used to obtain information on plant height, biomass, and leaf area. A visible and near-infrared (VNIR) HSI camera provided detailed spectral information for deriving spectral indices including the Normalised Difference Vegetation Index (NDVI), Photochemical Reflectance Index (PRI) and Normalized Difference Red Edge (NDRE). Manual measurements provided baseline comparative data. The 3D-multispectral scanner reliably estimated above-ground traits, with high correlations between manual and scanner-derived measurements. The ML models accurately differentiated among environmental stress treatments, with the fused 3D+HSI model achieving the best overall predictive performance across all evaluated metrics compared with models based on either imaging modality alone. Results demonstrated the effectiveness of combining 3D-multispectral and 2D-HSI data with ML analyses for non-destructive, high-throughput phenotyping. The integration of these techniques enabled non-destructive, high-throughput identification of environmental stress treatments imposed during plant growth.

plant biology↗

bioRxiv2024

Altered Expression of microRNAs Implicated in Hematopoietic Dysfunction in the Extracellular Vesicles of Bone Marrow-Mesenchymal Stromal Cells in Aplastic Anemia

Recently, we have reported that extracellular vesicles (EVs) from the bone marrow mesenchymal stromal cells (BM-MSC) of aplastic anemia (AA) patients inhibit hematopoietic stem and progenitor cell (HSPC) proliferative and colony-forming ability and promote apoptosis. One mechanism by which AA BM-MSC EVs might contribute to these altered HSPC functions is through microRNAs (miRNAs) encapsulated in EVs. However, little is known about the role of BM-MSC EVs derived miRNAs in regulating HSPC functions in AA. Therefore, we performed miRNA profiling of EVs from BM-MSC of AA (n=6) and normal controls (NC) (n=6), to identify differentially expressed miRNAs carried in AA BM-MSC EVs. DEseq2 analysis identified 34 significantly altered mature miRNAs in AA BM-MSC EVs. Analysis of transcriptome dataset of AA HSPC genes identified that 235 differentially expressed HSPC genes were targeted by these 34 EV miRNAs. The pathway enrichment analysis of 235 HSPC genes revealed their involvement in pathways associated with cell cycle, proliferation, apoptosis, and hematopoiesis regulation, thus highlighting that AA BM-MSC EV miRNAs could potentially contribute to impaired HSPC functions in AA.

molecular biology↗

bioRxiv2023

Pectin methylesterification modulates cell wall properties to promote neighbour proximity-induced hypocotyl growth

Plants growing with neighbours compete for light and consequently increase growth of their vegetative organs to enhance access to sunlight. This response, called shade avoidance syndrome (SAS), involves photoreceptors such as phytochromes as well as phytochrome interacting factors (PIFs), which regulate the expression of growth-mediating genes. Numerous cell wall-related genes belong to the putative targets of PIFs, and the importance of cell wall modifications for enabling growth was extensively shown in developmental models such as dark-grown hypocotyl. However, the role of the cell wall in the growth of de-etiolated seedlings regulated by shade cues remains poorly established. Through analyses of mechanical and biochemical properties of the cell wall coupled with transcriptomic analysis of cell wall-related genes, we show the importance of cell wall modifications in neighbour proximity-induced elongation. Further analysis using loss-of-function mutants impaired in the synthesis and remodeling of the main cell wall polymers corroborated this. We focused on the cgr2cgr3 double mutant that is defective in homogalacturonan (HG) methyltransferase activity required for methylesterification of HG-type pectins. By following hypocotyl growth kinetically and spatially and analyzing the mechanical and biochemical properties of cell walls, we found that methylesterification of HG-type pectins was required to enable global cell wall modifications. Moreover, HG-class pectin modification was needed for plant competition-induced hypocotyl growth. Collectively our work suggests that in the hypocotyl PIFs orchestrate changes in the expression of numerous cell wall genes to enable neighbour proximity-induced growth. One sentence summaryThe degree of methylesterification of pectins modulates global changes in the cell wall and its mechanical properties that contribute to the neighbour proximity-induced hypocotyl growth in Arabidopsis

plant biology↗

bioRxiv2022

Inhibiting Runx1 protects heart function after myocardial infarction

Myocardial infarction is a major cause of death worldwide. Effective treatments are required that limit adverse cardiac remodelling and preserve cardiac contractility following myocardial infarction, with the aim of improving patient outcomes and preventing progression to heart failure. The perfused but hypocontractile myocardium bordering a newly created infarct is functionally distinct from the remote surviving myocardium; it is also a major determinant of adverse cardiac remodelling and whole heart contractility. Expression of the transcription factor RUNX1 is increased in the border zone at 1 day after myocardial infarction, suggesting potential for targeted therapeutic intervention. Here we demonstrate that RUNX1 drives reductions in cardiomyocyte contractility, sarcoplasmic reticulum-mediated calcium release, mitochondrial density, and the expression of genes important for oxidative phosphorylation. Antagonising RUNX1 expression via short-hairpin RNA interference preserved cardiac contractile function following myocardial infarction when delivered either via direct adenoviral delivery into the border zone or via an adeno-associated virus vector administered intravenously. Equivalent effects were obtained with a small molecule inhibitor (Ro5-3335) that reduces RUNX1 function by blocking its interaction with the essential co-factor CBF{beta}. Both tamoxifen-inducible Runx1-deficient and Cbf{beta}-deficient cardiomyocyte-specific mouse models demonstrated that antagonising RUNX1 function preserves the expression of genes important for oxidative phosphorylation following myocardial infarction. Our results confirm the translational potential of RUNX1 as a novel therapeutic target in myocardial infarction, with wider opportunities for use across a range of cardiac diseases where RUNX1 drives adverse cardiac remodelling.

pathology↗