Biology subjects

Pal, N.

Publications and source records attributed to Pal, N..

8 recordsLinked to original sources

bioRxiv2025

TDP-43 pathology triggers SRRM4-dependent cryptic splicing of G3BP1 in ALS/FTD

Loss of nuclear TDP-43 is a defining feature of the neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), yet how this leads to selective neuronal vulnerability is poorly understood. Here, using human iPSC-derived neurons and a large multi-omics dataset of ALS/FTD patients, we demonstrate that TDP-43 pathology induces the inclusion of an in-frame cryptic exon in human G3BP1. The resulting CRYPTIC G3BP1 protein contains an additional 10-amino acids within the highly conserved NTF2L domain, which acts as a dominant negative and disrupts stress granule dynamics. We further show that cryptic exon inclusion in G3BP1 upon TDP-43 loss is enriched in neurons. Mechanistically, the loss of TDP-43 unmasks a binding site for the neuron-specific splicing regulator SRRM4 within intron 2 of G3BP1, enabling the inclusion of the cryptic exon. Collectively, our findings reveal that neuron-specific regulatory mechanisms intersect with TDP-43 -mediated splicing and suggest a mechanistic basis for the increased neuronal vulnerability observed in ALS/FTD.

neuroscience↗

bioRxiv2024

Framework for Martini-based Coarse-grained Model of Enzymes: Model Development and Experimental Validation

Recent experiments have shown that enzyme activity can preserved in harsh environments by complexing enzyme with polymer into a Protein-Polymer Hybrid (PPH). In a successful PPH, heteropolymer strands bind to the enzyme surface and restrain the folded protein without adversely affecting the binding and active sites. It is believed that hybridization is driven by non-covalent interactions at the enzyme surface including hydrophobicity and electrostatics. Molecular modeling of these interactions is not practical at the all-atom scale due to the long timescales and large particle counts needed to characterize binding. Protein structure at the scale of amino acid residues is parsimoniously represented by a coarse-grained model in which one particle represents several atoms, significantly reducing the cost of simulation. In this study we present two coarse-grained enzyme models - lipase and dehalogenase - prepared using a top-down modeling strategy. We simulate each enzyme in aqueous solution and calculate statistics of protein surface features and shape descriptors. The values from the coarse-grained data are compared with the same calculations performed on all-atom reference systems, revealing key similarities of surface chemistry at the two scales. Structural measures are calculated from the all-atom reference systems and compared with estimates from small-angle X-ray scattering (SAXS) experiments, with good agreement between the two. The described procedures of modeling and analysis comprise a framework for the development of coarse-grained models of protein surfaces with validation to experiment.

biophysics↗

bioRxiv2024

Preferential binding of human BRCA1 protein with open X-like conformation of Holliday junction, a homologous recombination intermediate

BRCA1 is a complex tumor suppressor protein involved in multiple critical cellular processes, e.g., DNA double strand break repair, cell cycle checkpoint, etc. BRCA1 depleted cells are reported to have decreased homologous recombination (HR) and promote error-prone non-homologous end joining for DNA damage repair. Holliday junction (HJ) is an important intermediate of HR. Although BRCA1 is shown to have a very high affinity for HJ and recruits several proteins at the DNA damage site, the question remains what the binding mode of BRCA1 protein with an HJ is. Using single-molecule Fluorescence Correlation Spectroscopy (FCS) we have shown that BRCA1 prefers an open X-like conformation of HJ and has a lesser affinity for stacked HJ. Further, using molecular docking and all-atom molecular dynamics simulation, we show that mostly charged and polar amino acids in the DNA binding region of BRCA1 form complex with HJ. Interestingly, most of those amino acids are reported to be places for missense changes.

biophysics↗

bioRxiv2024

Dirichlet distribution parameter estimation with application in microbiome analyses

Microbiomes are of vital importance for understanding human and environmental health. However, quantifying microbial composition remains challenging and relies on statistical modeling of either the raw taxonomic counts or the relative abundances. Relative abundance measures are commonly preferred over the absolute counts to analyze and interpret microbiome (as the sampling fraction are unknown in sequence data) but currently there is no ideal distribution for carrying out this modeling . In this work, the Dirichlet distribution is proposed to model the relative abundances of taxa directly without the use of any further transformation. In a comprehensive simulation study, we compared biases and standard errors of two Methods of Moments Estimators (MMEs) and Maximum Likelihood Estimator (MLE) of the Dirichlet distribution. Comparison of each estimator is done over three different cases of differing sample size and dimension: (i) small dimension and small sample size; (ii) small dimension and large sample size; (iii) large dimension with both large and small sample size. We demonstrate the Dirichlet modeling methodology with four real world microbiome datasets and show how the results of the Dirichlet model differ from those obtained by a commonly used method, namely Bayesian Dirichlet-Multinomial estimation (BDME). We find that the results of parameter estimation can be dependent upon the sequencing depth and sequencing technique used to produce a given microbiome dataset. However, for all datasets, the Dirichlet MLE (DMLE) results are comparable to the BDME results while requiring less computational time in each case.

bioinformatics↗

bioRxiv2023

Inactivation of Highly Transmissible Livestock and Avian Viruses Including Influenza A and Newcastle Disease Virus for Molecular Diagnostics

There is a critical need for an inactivation method that completely inactivates pathogens at the time of sample collection but maintains the nucleic acid quality required for diagnostic PCR testing. This inactivation method is needed to alleviate concerns about transmission potential, reduce shipping complications and cost, and allow testing in lower containment laboratories to improve disease diagnostics by improving turn-around time. This study evaluated a panel of ten surrogate viruses that represent highly pathogenic animal diseases. These results showed that a commercial (PrimeStore(R)) molecular transport media (PSMTM) completely inactivated all viruses tested by >99.99% as determined by infectivity and serial passage assays. However, detection of viral nucleic acid by qRT-PCR was comparable in PSMTM and control-treated conditions. These results were consistent when viruses were evaluated in the presence of biological material such as sera and cloacal swabs to mimic diagnostic sample conditions for non-avian and avian viruses, respectively. The results of this study may be utilized by diagnostic testing laboratories for highly pathogenic agents affecting animal and human populations. These results may be used to revise guidance for select agent diagnostic testing and shipment of infectious substances. Contribution to the fieldActive surveillance and confirmatory testing efforts are in place to protect animals in the United States from certain highly contagious diseases and to limit financial impacts to consumers and producers when the food supply is disrupted. Confirmatory testing typically utilizes nucleic acid detection to identify active infection. Testing is required to be completed in high containment facilities due to the elevated pathogenicity and impact potential of animal diseases. The requirement for testing in high containment facilities limits the ability for regional and state laboratories to test for Tier 1 select agents. Shipment of diagnostic samples is costly, as well as time and temperature sensitive to avoid deterioration of sample quality needed for testing. These constraints lengthen response time and testing turn-around time. Here, we showed that a commercial (PrimeStore(R)) molecular transport media (PSMTM) completely inactivated all viruses tested without affecting nucleic acid detection/integrity. These data suggest that highly contagious agents are effectively inactivated by PSMTM without compromising the nucleic acid needed for diagnostic testing. These data provide support that this inactivation method can be utilized during sample collection to reduce constraints in disease diagnostics and in reagent sharing among international laboratories.

microbiology↗

bioRxiv2023

Confined environment facilitates stacked conformations in Holliday Junction

Holliday Junction (HJ) is an important intermediate for homologous recombination and is involved in DNA break repair. It is a highly dynamic structure and transitions between two stacked isomers through an intermediate open conformer. In a constrained cellular environment, HJ is expected to behave differently than in vitro. This can affect target recognition by junction-binding proteins and their subsequent functions. However, the studies on the effect of the confined environment on HJ is extremely scanty. In this work, by employing fluorescence-based techniques we investigated the effect of confinement on HJ conformation using reverse micelle encapsulation as a model for confined space. We observed that inside reverse micelle, HJ prefers to adopt stacked conformation. Most strikingly, even at lower divalent cation concentrations, the preference for stacked conformation is prevalent over an open conformation. Our finding suggests that such confinement-induced changes in the conformer population might affect the interaction and activity of the HJ-recognizing proteins in the cellular environment.

biophysics↗

bioRxiv2022

Consensus genomic regions associated with multiple abiotic stress tolerance in wheat and implications for wheat breeding

In wheat, a meta-analysis was performed using previously identified QTLs associated with drought stress, heat stress, salinity stress, water-logging stress, pre-harvest sprouting, and aluminium stress which predicted a total of 134 meta-QTLs (MQTLs) that involved at least 28 consistent and stable MQTLs conferring tolerance to five or all six abiotic stresses under study. Seventy-six MQTLs out of the 132 physically anchored MQTLs were also verified with genome-wide association studies. Around 43% of MQTLs had genetic and physical confidence intervals of less than 1 cM and 5 Mb, respectively. Consequently, 539 genes were identified in some selected MQTLs providing tolerance to 5 or all 6 abiotic stresses. Comparative analysis of genes underlying MQTLs with four RNA-seq based transcriptomic datasets unravelled a total of 191 differentially expressed genes which also included at least 11 most promising candidate genes common among different datasets. The promoter analysis showed that the promoters of these genes include many stress responsiveness cis-regulatory elements, such as ARE, MBS, TC-rich repeats, As-1 element, STRE, LTR, WRE3, and WUN-motif among others. Further, some MQTLs also overlapped with as many as 34 known abiotic stress tolerance genes. In addition, numerous ortho-MQTLs among the wheat, maize, and rice genomes were discovered. These findings could help with fine mapping and gene cloning, as well as marker-assisted breeding for multiple abiotic stress tolerances in wheat.

bioinformatics↗

bioRxiv2019

Metabolic Profiling of Aortic Stenosis and Hypertrophic Cardiomyopathy Identifies Mechanistic Contrasts in Substrate Utilisation

BackgroundAortic stenosis (AS) and hypertrophic cardiomyopathy (HCM) are highly distinct disorders leading to left ventricular hypertrophy (LVH), but whether cardiac metabolism substantially differs between these in humans remains to be elucidated.\n\nMethodWe undertook a detailed invasive (aortic root and coronary sinus) metabolic profiling in patients with severe AS and HCM in comparison to non-LVH controls, to investigate cardiac fuel selection and metabolic remodelling. These patients were assessed under different physiological states (at rest and during stress induced by pacing). The identified changes in the metabolome were further validated by metabolomic and orthogonal transcriptomic analysis, in separately recruited patient cohorts.\n\nResultsWe identified a highly discriminant metabolomic signature in severe AS characterised by striking accumulation of long-chain acylcarnitines, intermediates of long-chain transport and fatty acid metabolism, and validated this in a separate cohort. Mechanistically, we identify a down-regulation in the PPAR- transcriptional network, including expression of genes regulating FAO.\n\nConclusionsWe present a comprehensive analysis of changes in the metabolic pathways (transcriptome to metabolome) in severe AS, and its comparison to HCM. Our results demonstrate fundamental distinctions in substrate preference between AS and HCM, highlighting insufficient long-chain FAO, and the PPAR- signalling network as a specific metabolic therapeutic target in AS.

systems biology↗