Biology subjects

Samalova, M.

Publications and source records attributed to Samalova, M..

6 recordsLinked to original sources

bioRxiv2024

The molecular core of transcriptome responses to abiotic stress in plants: a machine learning-driven meta-analysis

Understanding how plants adapt their physiology to overcome severe stress conditions is vital in light of the current climate crisis. This remains a challenge given the complex nature of the underlying molecular mechanisms. To provide a full picture of stress mitigation mechanisms, an exhaustive analysis of publicly available stress-related transcriptomic data was conducted. We combined a meta-analysis with an unsupervised machine learning algorithm to identify a core of stress-related genes. To ensure robustness and biological significance of the output, often lacking in meta-analyses, a three-layered biovalidation was incorporated. Our results present a stress gene core, a set of key genes involved in plant tolerance to a multitude of adverse environmental conditions rather than specific ones. In addition, we provide a biologically validated database to assist in design of multi-stress resilience. Taken together, our results pave the way towards future-proof sustainable agriculture. TeaserUsing a machine learning-driven meta-analysis, a plant stress gene core was identified as a hub mediating multi-stress regulation

plant biology↗

bioRxiv2023

Imaging the microscopic viscoelastic anisotropy in living cells

Maintaining and modulating the mechanical anisotropy is essential for biological processes. How this is achieved on the microscopic scale in living soft matter is however not always clear. Here we introduce Brillouin Light Scattering Anisotropy Microscopy (BLAM) for mapping the high-frequency viscoelastic anisotropy inside living cells. Following proof-of-principle experiments on muscle myofibers, we apply this to study two fundamental biological processes. In plant cell walls we show how a phase-transition driven switch between anisotropic-isotropic wall properties may lead to asymmetric growth. In mammalian cell nuclei we uncover a spatio-temporally oscillating elastic anisotropy correlated to chromatin condensation, with long range orientational correlations that may provide a dynamic framework for coordinating intra-nuclear processes. Our results highlight the direct and indirect role the high-frequency mechanics can play in providing dynamic structure that lead to the regulation of diverse fundamental processes in biological systems, and offer a means for studying these. BLAM should find diverse biomedical and material characterization applications.

biophysics↗

bioRxiv2022

Characterisation of organised smooth endoplasmic reticulum suggests a route towards synthetic compartmentalisation

Engineering of subcellular compartmentalisation is one of synthetic biologys key challenges. Among different approaches, de novo construction of a synthetic compartment is the most coveted but also most difficult option. Restructuring the endoplasmic reticulum (ER), via the introduction of recombinant oligomerising ER-membrane resident proteins, is an alternative starting point for building a new compartment. The presence of such proteins leads to a massive expansion of the ER and the formation of organised smooth endoplasmic reticulum (OSER), a large membranous compartment. However, OSER is poorly characterised and our understanding of its effect on the underlying biology of the plant is limited. Here we characterise a range of OSER compartments and show how the structure of the inducing polyprotein constructs affect the final compartment morphology, with the cytosolic-facing antiparallel oligomerisation domain demonstrated to be an essential component to trigger OSER formation. We show that while OSER retains a connection to the ER, a diffusional barrier exists to both the ER and the cytosol. Using high-resolution quantitative image analysis, we also show that the presence of this large compartment does not disrupt the rest of the ER network. Moreover, transgenic Arabidopsis constitutively expressing the compartment-forming polyproteins grew and developed normally. These properties collectively suggest that OSER could be developed as a plant synthetic biology tool for compartmentalisation, combining the benefits of several existing strategies. Only a single protein construct is necessary to induce its formation, and the compartment retains a delimiting membrane and a diffusional barrier to the rest of the cell.

plant biology↗

bioRxiv2021

The steroid-inducible pOp6/LhGR gene expression system is fast, sensitive and does NOT cause plant growth defects in rice (Oryza sativa)

Inducible systems for transgene expression activated by a chemical inducer or an inducer of non-plant origin are desirable tools for both basic plant research and biotechnology. Although, the technology has been widely exploited in model plants, it has not been optimised for use with the major monocotyledonous crop species, namely rice. We have adapted the dexamethasone-inducible pOp6/LhGR system for rice and shown that it is fast, sensitive and tightly regulated, with high levels of induction that remain stable over several generations. Most importantly, we have shown that the system does not cause negative growth defects in vitro or in soil grown plants. Interestingly in the process of testing, we found that another steroid, triamcinolone acetonide, is a more potent inducer in rice than dexamethasone. We present serious considerations for the construct design to avoid undesirable effects caused by the system in plants, leakiness and possible silencing, as well as simple steps how to maximize translation efficiency of a gene of interest. Finally, we compare the performance of the pOp6/LhGR system with other chemically inducible systems tested in rice in terms of the properties of an ideal inducible system. Significance statementThe non-monocot codon-optimized version of the dexamethasone inducible pOp6/LhGR system does not cause severe developmental perturbations in rice plants.

plant biology↗

bioRxiv2020

Expansin-controlled cell wall stiffness regulates root growth in Arabidopsis

Expansins facilitate cell expansion via mediating pH-dependent cell wall (CW) loosening. However, the role of expansins in the control of biomechanical CW properties in the tissue and organ context remains elusive. We determined hormonal responsiveness and specificity of expression and localization of expansins predicted to be direct targets of cytokinin signalling. We found EXPA1 homogenously distributed throughout the CW of columella/ lateral root cap, while EXPA10 and EXPA14 localized predominantly at the three-cell boundaries of epidermis/cortex in various root zones. Cell type-specific localization of EXPA15 overlaps with higher CW stiffness measured via Brillouin light scattering microscopy. As indicated by both Brillouin frequency shift and AFM-measured Youngs modulus, EXPA1 overexpression upregulated CW stiffness, associated with shortening of the root apical meristem and root growth arrest. We propose that root growth in Arabidopsis requires delicate orchestration of biomechanical CW properties via tight regulation of various expansins localization to specific cell types and extracellular domains.

plant biology↗

bioRxiv2019

Optimization of a Modular Steroid-Inducible Gene Expression System for Use in Rice

Chemically inducible systems that provide both spatial and temporal control of gene expression are essential tools, with many applications in plant biology. Using Golden Gate modular cloning, we have created a monocot-optimized dexamethasone (DEX)-inducible pOp6/LhGR system and tested its efficacy in rice using the reporter enzyme {beta}-glucuronidase (GUS). The system is tightly regulated and highly sensitive to DEX application, with six hours of induction sufficient to induce high levels of GUS activity in transgenic callus. In seedlings, GUS activity was detectable in the root after in vitro application of just 0.01M DEX. However, transgenic plants manifested severe developmental perturbations when grown on higher concentrations of DEX. The direct cause of these growth defects is not known, but the rice genome contains sequences with high similarity to the LhGR target sequence lacO, suggesting non-specific activation of endogenous genes by DEX induction. These off-target effects can be minimized by quenching with isopropyl {beta}-D-1-thiogalactopyranoside (IPTG). The system is thus suitable for general use in rice, when the method of DEX application and relevant controls are tailored appropriately for each specific application.

plant biology↗