Biology subjects

Mitra, M.

Publications and source records attributed to Mitra, M..

8 recordsLinked to original sources

bioRxiv2026

P2X7 receptor antagonism potentiates seizure-suppressive effects of anti-seizure medications in human resected epileptic brain tissue

Resistance to anti-seizure medications (ASMs) remains a major clinical challenge in the management of epilepsy. Neuroinflammation has been implicated as a contributing mechanism and, consistent with this, antagonists of the ATP-gated P2X7 receptor (P2X7R) have been shown to enhance ASM efficacy in animal models. It remains unclear, however, if P2X7R antagonism is effective in human models of drug-resistant epilepsy. Here, we assessed the seizure-suppressive potential of the P2X7R antagonists AFC-5128 and JNJ-47965567 using electrophysiological recordings in acute resected brain slices from patients with epilepsy using artificial cerebrospinal fluid containing low Mg2+ and high K+ to evoked seizure-like events. P2X7R antagonists alone did not suppress seizure-like activity. When co-administered, however, P2X7R antagonists significantly enhanced the anti-seizure efficacy of carbamazepine and lorazepam. Notably, P2X7R antagonist treatment lowered Interleukin-1{beta} levels, and betaine, a drug targeting Interleukin-1{beta} release, mimicked the effects of P2X7R antagonists when combined with carbamazepine. Finally, mice with microglia-specific P2X7R depletion showed improved responsiveness to carbamazepine, suggesting P2X7R-mediated effects are partially mediated via their functions in microglia. These findings suggest that P2X7R-based therapies may represent an effective add-on approach for treating drug-resistant seizures associated with neuroinflammation.

neuroscience↗

bioRxiv2026

Far-from-equilibrium assembly of multimers through DNA-based catalytic templating

On-demand assembly of arbitrary, sequence-defined polymers from a pool of monomers is a major challenge in modern chemistry, towards which limited progress has been made. By contrast, biological systems routinely use information-bearing DNA and RNA templates to catalytically synthesize a precise, far-from-equilibrium ensemble of nucleic acid and protein sequences from the available pools of nucleoside triphosphates or aminoacyl-tRNAs. Inspired by these biological examples, we introduce an enzyme-free DNA strand displacement network in which single-stranded DNA sequences template the assembly of specific non-covalent DNA multimers of up to length five, under isothermal and autonomous conditions. The templates overcome product inhibition and can thereby catalyse the formation of a far-from-equilibrium ensemble of long-lived metastable products that are not otherwise addressable.

biophysics↗

bioRxiv2026

Fuel-driven catalytic molecular templating

Catalytic molecular templating, wherein a copolymer molecule serves as a sequence-specific template to propagate genetic information to a daughter copolymer, is fundamental to cells. Templating underlies DNA replication, RNA transcription and protein translation, underpinning the molecular basis of heredity, evolution, and biological function, and allowing staggering complexity to arise from simple building blocks. It has hitherto been challenging to emulate templating without highly evolved enzymes, largely due to product inhibition of catalytic turnover, which is a major challenge for templated dimerization and prohibitive for longer products. We present an enzyme-free DNA-based templated dimerization reaction enabled and controlled by a fuel strand that actively displaces the product from the template only once dimerization is complete, overcoming product inhibition. We systematically investigate design variants to optimise catalytic turnover, and demonstrate information propagation through the action of distinct templates that assemble specific products from the same pool of building blocks. We also show that the fuel represents an input by which the templating can be controlled, allowing the coupling of catalytic turnover to the output of upstream DNA circuitry. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/706517v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@e82eeeorg.highwire.dtl.DTLVardef@1612b85org.highwire.dtl.DTLVardef@706911org.highwire.dtl.DTLVardef@217d6_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2026

H4K20me3 and CTCF act reciprocally at TAD boundaries to regulate cell state transitions

Reversible transitions between proliferative and quiescent cell states involve widespread gene expression changes despite stable topologically associating domain (TAD) boundaries. We report a reciprocal antagonism between TAD boundary element CTCF and histone modification H4K20me3 as a central mechanism governing the proliferation-quiescence transition. Genome-wide studies and functional perturbations reveal that elevated H4K20me3 in quiescent fibroblasts displaces CTCF at specific TAD boundaries while CTCF binding predominates in proliferating cells. Increased H4K20me3 reversibly induces a compact chromatin state, elliptical nuclear morphology, and transcriptional programs associated with quiescence. Conversely, elevated CTCF binding drives open chromatin, proliferative gene expression, and cell division despite quiescence signals. Fibroblasts lacking H4K20me3 methyltransferase KMT5C/Suv4-20h2 are hyper-proliferative and KMT5C-deficient mice are larger. Our findings provide a mechanistic framework for how architectural and epigenetic regulators exchange at TAD boundaries to coordinate reversible cell state transitions, a finding with implications for organismal development and diseases of dysregulated proliferation.

cell biology↗

bioRxiv2025

Xylan modifications in Populus that lead to increased growth

Xylem cells are surrounded by primary and secondary cell walls. Formation of primary walls is regulated by the cell wall integrity surveyance system, but it is unclear if the deposition of secondary walls is similarly regulated. To study this question, we introduced to aspen three different enzymes cleaving cell wall-localized xylan and we suppressed xylan synthase components either ubiquitously or specifically during secondary wall formation. When xylan was ubiquitously altered, 95% of lines showed reduced growth, whereas when it was altered during secondary wall deposition, 30% of lines grew better with the rest having no growth impairment, suggesting opposite effects of primary and secondary wall disturbances. To detect mechanism of growth stimulation by disturbed deposition of secondary wall, we analyzed changes in wood quality traits, chemistry, transcriptomics, metabolomics and hormonomics in transgenic lines. We found increased tension wood production, reduced S- and H-lignin, and changes in several metabolites in common in these lines. Remorin REM1.3 and NRL2 (NPH3 family) transcripts increased and changes in jasmonates, ABA and SA occurred in secondary wall-forming xylem suggesting their involvement in secondary wall integrity surveyance and signaling. The data indicate that a unique program mediates responses to secondary wall impairment that induces growth. HighlightDisturbance of the deposition of secondary walls that are responsible for the mechanical strength of plant bodies can increase growth with discrete changes in gene expression, hormone levels and metabolism.

plant biology↗

bioRxiv2024

Modification of xylan in secondary walls alters cell wall biosynthesis and wood formation programs

Wood of broad-leaf tree species is a valued source of renewable biomass for biorefinery and a target for genetic improvement efforts to reduce its recalcitrance. Glucuronoxylan (GX) plays a key role in recalcitrance through its interactions with cellulose and lignin. To reduce recalcitrance, we modified wood GX by expressing GH10 and GH11 endoxylanases from Aspergillus nidulans in hybrid aspen (Populus tremula L. x tremuloides Michx.) and targeting the enzymes to cell wall. The xylanases reduced tree height, modified cambial activity by increasing phloem and reducing xylem production, and reduced secondary wall deposition. Xylan molecular weight was decreased, and the spacing between acetyl and MeGlcA side chains was reduced in transgenic lines. The transgenic trees produced hypolignified xylem having thin secondary walls and deformed vessels. Glucose yields of enzymatic saccharification without pretreatment almost doubled indicating decreased recalcitrance. The transcriptomics, hormonomics and metabolomics data provided evidence for activation of cytokinin and ethylene signaling pathways, decrease in ABA levels, transcriptional suppression of lignification and a subset of secondary wall biosynthetic program, including xylan glucuronidation and acetylation machinery. Several candidate genes for perception of impairment in xylan integrity were detected. These candidates could provide a new target for uncoupling negative growth effects from reduced recalcitrance. In conclusion, our study supports the hypothesis that xylan modification generates intrinsic signals and evokes novel pathways regulating tree growth and secondary wall biosynthesis.

plant biology↗

bioRxiv2023

Immunoproteasome deficiency results in accelerated brain aging and epilepsy

The immunoproteasome is a central protease complex required for optimal antigen presentation. Immunoproteasome activity is also associated with facilitating degradation of misfolded and oxidized proteins, which prevents cellular stress. While extensively studied during diseases with increasing evidence suggesting a role for the immunoproteasome during pathological conditions including neurodegenerative diseases, this enzyme complex is believed to be mainly inactive in the healthy brain. Here, we show an age-dependent increase in polyubiquitination in the brain of wild-type mice, accompanied with induction of immunoproteasomes, which was most prominent in neurons and microglia. In contrast, mice completely lacking immunoproteasomes (triple-knockout (TKO) mice deficient for LMP2, LMP7 and MECL-1), displayed a strong increase in polyubiquitinated proteins already in the young brain and developed spontaneous epileptic seizures, beginning at the age of 6 months. Injections of kainic acid led to high epilepsy-related mortality of aged TKO mice, confirming increased pathological hyperexcitability states. Notably, the expression of the immunoproteasome was reduced in the brains of patients suffering from epilepsy. In addition, aged TKO mice showed increased anxiety, tau hyperphosphorylation and degeneration of Purkinje cell population with the resulting ataxic symptoms and locomotion alterations. Collectively, our study suggests a critical role for the immunoproteasome in the maintenance of a healthy brain during aging.

neuroscience↗

bioRxiv2019

Cyto-architecture constrains a photoactivation induced tubulin gradient in the syncytial Drosophila embryo

Drosophila embryogenesis begins with nuclear division in a common cytoplasm forming a syncytial cell. Morphogen gradient molecules spread across nucleo-cytoplasmic domains to pattern the body axis of the syncytial embryo. The diffusion of molecules across the syncytial nucleo-cytoplasmic domains is potentially constrained by association with the components of cellular architecture, however the extent of restriction has not been examined so far. Here we use photoactivation (PA) to generate a source of cytoplasmic or cytoskeletal molecules in order to monitor the kinetics of their spread in the syncytial Drosophila embryo. Photoactivated PA-GFP and PA-GFP-Tubulin within a fixed anterior area diffused along the antero-posterior axis. These molecules were enriched in cortical cytoplasm above the yolk-filled center suggesting that the cortical cytoplasm is phase separated from the yolk-filled center. The length scales of diffusion were extracted using exponential fits under steady state assumptions. PA-GFP spread to greater distance as compared to PA-GFP-Tubulin. Both gradients were steeper and more restricted when generated in the center of the embryo probably due to a higher density of nucleo-cytoplasmic domains. The length scale of diffusion for PA-GFP-Tubulin gradient increased in mutant embryos containing short plasma membrane furrows and disrupted tubulin cytoskeleton. The PA-GFP gradient shape was unaffected by cyto-architecture perturbation. Taken together, these data show that PA-GFP-Tubulin gradient is largely restricted by its incorporation in the microtubule network and intact plasma membrane furrows. This photoactivation based analysis of protein spread across allows for interpretation of the dependence of gradient formation on the syncytial cyto-architecture.

developmental biology↗