Biology subjects

Maji, D.

Publications and source records attributed to Maji, D..

4 recordsLinked to original sources

bioRxiv2026

Quantifying RNA Folding Equilibria from Unclassified Cryo-EM Particle Images

Functional RNA structures are typically far more dynamic than most proteins solved by cryo-electron microscopy (cryo-EM). Flexible junctions and weak tertiary contacts produce broad conformational ensembles, and cryo-EM particle classification analyses discard unaligned particles, which inherently contain the information needed to quantify such broad ensembles. Here, we infer compositional and conformational distributions from unclassified particle images by Bayesian ensemble reweighting. We tested our approach on the P4-P6 domain of the Tetrahymena thermophila group I intron, a classic model system of Mg2+-dependent RNA folding. While stable monomeric and dimeric states yielded high-resolution reconstructions, analyses of abundant, flexible conformations required Bayesian ensemble inference. Our approach quantitatively captured the Mg2+-dependent folding transition, indicating that cryo-EM can report the abundance of coexisting RNA states in agreement with bulk solution measurements. These results showcase how quantitative studies of RNA folding can be achieved by combining cryo-EM measurements with statistical ensemble-inference tools.

biochemistry↗

bioRxiv2025

DNA-based delivery of incretin receptor agonists using MYO Technology leads to durable weight loss in a diet-induced obesity model

Therapeutic proteins have seen a substantial increase in clinical development and use across many disease areas. Despite their broad applicability, significant drawbacks limit access to many of these drugs, including: i) high manufacturing costs; ii) administration via time-consuming infusions; iii) frequent dosing, sometimes even daily; and iv) requirements for low temperature storage. MYO Technology was developed to overcome these barriers. The MYO Technology platform consists of therapeutic-encoding plasmid DNA (pDNA), and a proprietary medical device for intramuscular injection and delivery of electrical pulses. These pulses enable the in vivo electroporation of muscle cells and uptake of injected pDNA, leading to the production, secretion, and delivery of the therapeutic protein into peripheral circulation. MYO Technology offers several advantages over standard delivery of therapeutic proteins; pDNA manufacturing is a simpler and less specialized process compared to protein manufacturing, and pDNA is very stable and lacks most cold chain requirements. Furthermore, administration using MYO Technology takes only a few minutes, and the serum level of a therapeutic protein can potentially be maintained for many months without the need for redosing. Incretin receptor agonists (IRAs) are a class of therapeutic proteins that have recently come to prominence as powerful weight and glucose control drugs, and are used for the treatment of type 2 diabetes (T2D) and obesity. Semaglutide and tirzepatide, currently the most widely used within this class, are both potent molecules, but have a short half-life, requiring weekly administration by subcutaneous injections. Moreover, since their clinical benefits rapidly disappear upon treatment cessation, T2D and obese patients may have a life-long dependency on IRAs, and the requirement for weekly injections can negatively affect the quality of life and the adherence to therapy, as well as create a significant financial burden. Therefore, increasing the interval between injections has become one of the major goals in the field. Here, we present our preclinical studies on the delivery of IRAs with MYO Technology. Animal proof-of-concept studies demonstrate that MYO Technology-delivered IRAs are functional, and efficacious in promoting long-lasting weight and glucose control in mouse models of diet-induced obesity. Moreover, engineering the IRAs to facilitate blood-brain barrier penetration further enhances treatment efficacy, with benefits persisting beyond one year following a single administration. Together, these findings highlight MYO Technologys potential to transform care for patients with T2D and obesity by enabling long-lasting therapeutic effects with minimal dosing, ultimately improving quality of life and treatment adherence.

physiology↗

bioRxiv2023

Genetic Variations and Altered Blood mRNA Level of Circadian Genes and BDNF as Risk Factors of Post-Stroke Cognitive Impairment among Eastern Indians

BackgroundPost-stroke cognitive impairment (PSCI) is a clinical outcome in around 30% of post-stroke survivors. BDNF is a major gene in this regard. It regulates and being regulated by circadian rhythm. The circadian genes are correlated with stroke timings at molecular level. However, studies suggesting the role of these on susceptibility to PSCI is limited. AimWe aim here to determine a) genetic risk variants in circadian clock genes, BDNF and b) dysregulation in expression level of CLOCK, BMAL1 and BDNF, that may be associated with PSCI. MethodsBDNF (rs6265G/A, rs56164415C/T), CLOCK (rs1801260T/C, rs4580704G/C) and CRY2 (rs2292912C/G) genes variants were genotyped among 119 post-stroke survivors and 292 controls from Eastern part of India. In addition, we analysed their gene expression in PBMC from 15 PSCI cases and 12 controls. The mRNA data for BDNF was further validated by its plasma level through ELISA. ResultsAmong the studied variants, only rs4580704/CLOCK showed an overall association with PSCI (P = 0.001) and lower BMSE score. Its C allele showed a correlation with attention deficiency. The language and memory impairments showed association with rs6265/BDNF while the CC genotype of rs2292912/CRY2 negatively influenced language and executive function. A significant decrease in gene expression for CLOCK and BDNF in PBMC (influenced by specific genotypes) of PSCI patients was observed than controls. Unlike, Pro-BDNF, plasma level mBDNF was also lower in them. ConclusionsOur results suggest that the circadian genes and BDNF play a role in PSCI on both genetic and transcript level.

neuroscience↗

bioRxiv2021

Pre-mRNA Splicing Factor U2AF2 Recognizes Distinct Conformations of Nucleotide Variants at the Center of the pre-mRNA Splice Site Signal

The essential pre-mRNA splicing factor U2AF2 (also called U2AF65) identifies polypyrimidine (Py) tract signals of nascent transcripts, despite length and sequence variations. Previous studies have shown that the U2AF2 RNA recognition motifs (RRM1 and RRM2) preferentially bind uridine-rich RNAs. Nonetheless, the specificity of the RRM1/RRM2 interface for the central Py tract nucleotide has yet to be investigated. We addressed this question by determining crystal structures of U2AF2 bound to a cytidine, guanosine, or adenosine at the central position of the Py tract, and compared U2AF2-bound uridine structures. Local movements of the RNA site accommodated the different nucleotides, whereas the polypeptide backbone remained similar among the structures. Accordingly, molecular dynamics simulations revealed flexible conformations of the central, U2AF2-bound nucleotide. The RNA binding affinities and splicing efficiencies of structure-guided mutants demonstrated that U2AF2 tolerates nucleotide substitutions at the central position of the Py tract. Moreover, enhanced crosslinking and immunoprecipitation of endogenous U2AF2 in human erythroleukemia cells showed uridine-sensitive binding sites with lower sequence conservation at the central nucleotide positions of otherwise uridine-rich, U2AF2-bound splice sites. Altogether, these results highlight the importance of RNA flexibility for protein recognition and take a step towards relating splice site motifs to pre-mRNA splicing efficiencies.

biophysics↗