Biology subjects

Saeed, S.

Publications and source records attributed to Saeed, S..

7 recordsLinked to original sources

bioRxiv2025

The DREAM complex links somatic mutation, lifespan, and disease

The DREAM complex has emerged as a central repressor of DNA repair, raising questions as to whether such repression exerts long-term effects on human health. Here we establish that DREAM activity significantly impacts lifetime somatic mutation burden, and that such effects are linked to altered lifespan and age-related disease pathology. First, joint profiling of DREAM activity and somatic mutations across a single-cell atlas of 21 mouse tissues shows that cellular niches with lower DREAM activity have decreased mutation rates. Second, DREAM activity predicts the varied lifespans observed across 92 mammals, with low activity marking longer-lived species. Third, reduced DREAM activity in Alzheimers patients predicts late disease onset and decreased risk for severe neuropathology. Finally, we show DREAM knockout protects against mutation accumulation in vivo, reducing single-base substitutions by 4.2% and insertion/deletions by 19.6% in brains of mice. These findings position DREAM as a key regulator of aging.

bioinformatics↗

bioRxiv2025

A Universal Duplex Sequencing Approach for Accurate Detection of Somatic Mutations

Ultra-accurate detection of rare somatic mutations is critical for understanding mutational processes in human disease, aging, and environmental exposures, yet current methods are limited by error rates, restricted genome coverage, and high DNA input. We present UDSeq, a duplex sequencing protocol combining random fragmentation, efficient UMI ligation, and quantitative input control to achieve near-complete genome/exome representation from as little as 100 pg DNA. Benchmarking in human sperm estimates a UDSeq error rate of [~]2.5x10-9 per base pair. UDSeq captures mutational signatures from heterogeneous populations without clonal expansion, reproduces exposure-specific patterns in cell lines and rodent models, and enables cross-species profiling. Compared with prior duplex methods, UDSeq yields up to fourfold more usable duplex molecules, improves library conversion, and remains cost-effective. We include a step-by-step protocol with quality-control checkpoints for fragment size, ligation yield, library conversion, and duplication rate. UDSeq provides a scalable, low-input platform for accurate profiling of somatic mutagenesis.

genomics↗

bioRxiv2025

Targeting ZNRF3 and RNF43 to Restore Regeneration and Reverse Metabolic Dysfunction-Associated Steatotic Liver Disease

Liver regeneration and hepatocyte metabolic identity are disrupted in metabolic dysfunction-associated steatotic liver disease (MASLD) and its advanced form, metabolic dysfunction-associated steatohepatitis (MASH), yet the mechanisms of restore liver regeneration and reprogram metabolism for disease reversal remains poorly understood. Here, we show that {beta}-Catenin activity progressively declines in hepatocytes during MASH in both humans and mice, coinciding with impaired regeneration and defective lipid clearance. Targeted deletion of the endogenous WNT pathway inhibitors ZNRF3 and RNF43 in hepatocytes after MASH onset reactivates {beta}-Catenin signaling, leading to robust regression of steatosis, inflammation, and fibrosis, and restoring regenerative capacity across multiple fatty liver disease models. Mechanistically, this therapeutic effect is driven by {beta}-Catenin-dependent induction of the alternative bile acid synthesis pathway without disrupting systemic lipid homeostasis. Importantly, both short-and long-term deletion of ZNRF3/RNF43 restores liver function without triggering tumorigenesis or hepatotoxicity, indicating a safe therapeutic window. These findings reveal that physiological activation of WNT/{beta}-catenin signaling via ZNRF3 and RNF43 offers a viable regenerative and metabolic strategy for reversing fatty liver disease.

cell biology↗

bioRxiv2025

Changes in biophysical characteristics of YghA from E. coli due to variation in pH

YghA from E. coli has been reported to be involved in conferring tolerance against furan aldehyde inhibitors which are commonly generated in thermo-acidic pretreatment of lignocellulosic biomass. In this study we report the biophysical characterization of YghA from E. coli as a function of variation in pH. Fluorescence intensity of YghA increased by 2.5-fold in acidic pH as compared to circumneutral pH. In presence of the hydrophilic 8-anilinonaphthalene-1-sulfonic acid (ANS) dye, a 68 - 79.4-fold increase in fluorescence intensity at acidic pH was observed as compared to circumneutral pH, while at basic pH the increase was only 1 to 2-fold. Secondary structure analysis by circular dichroism signal at 222 and 208 nm suggests that the secondary structure of YghA is primarily composed of alpha-helix at pH 7 and the secondary structure is abruptly lost at pH 3 and lower. In agreement with these observations, MD simulations predicted greater structural variations at low pH when compared to neutral or high pH. Interface energy calculations using computational docking protocols suggested that YghA forms relatively more stable complex with NADH. The in silico pulling assay results also show that NADH is more preferred compared to NADPH. Molecular dynamics simulations also indicate that YghA is structurally unstable at acidic pH with significant variations in the root mean square deviation values of the tetramer backbone. Residues GLU 84 at pH 7 together with PRO 24 and LEU 236 at pH 1 were identified as flexible residues and are promising target for future mutagenesis studies targeted towards improving structural stability of YghA.

biochemistry↗

bioRxiv2024

Automated cell tracking using 3D nnUnet and Light Sheet Microscopy to quantify regional deformation in zebrafish

Light Sheet Microscopy (LSM) in conjunction with embryonic zebrafish, is rapidly advancing three-dimensional, in vivo characterization of myocardial contractility. Preclinical cardiac deformation imaging is predominantly restricted to a low-order dimensionality image space (2i) or suffers from poor reproducibility. In this regard, LSM has enabled high throughput, non-invasive 4i (3d+time) characterization of dynamic organogenesis within the transparent zebrafish model. More importantly, LSM offers cellular resolution across large imaging Field-of-Views at millisecond camera frame rates, enabling single cell localization for global cardiac deformation analysis. However, manual labeling of cells within multilayered tissue is a time-consuming task and requires substantial expertise. In this study, we applied the 3i nnU-Net with Linear Assignment Problem (LAP) framework for automated segmentation and tracking of myocardial cells. Using binarized labels from the neural network, we quantified myocardial deformation of the zebrafish ventricle across 4-6 days post fertilization (dpf). Our study offers tremendous promise for developing highly scalable and disease-specific biomechanical quantification of myocardial microstructures.

bioengineering↗

bioRxiv2020

Biochemical profile and bioactive potential of wild folk medicinal plants of Zygophyllaceae from Balochistan, Pakistan.

Recent focus is on analysis of biological activities of extracts from plant species. Zygophyllaceae is exceedingly important angiosperm family with many taxa being used in folk medicines widely dispersed in arid and semi-arid zones of Balochistan, Pakistan. Only a small proportion of them have been scientifically analyzed and many species are nearly facing extinction. Therefore present investigation explores the biochemical and bioactive potential of fourteen folk medicinal plants usually used for treatments of different ailments. Fresh aerial parts of nine taxa and two fruit samples were collected from plants growing in arid and semi-arid zones of Balochistan and analyzed for enzymatic, non-enzymatic and other biochemical activities. Higher phytochemical activities were detected in the aerial parts. Superoxide dismutase was detected maximum in Fagonia indica, (184.7{+/-}5.17 units/g), ascorbate peroxidase in Tribulus longipetalus subsp. longipetalus (947.5{+/-}12.5 Units/g), catalase and peroxidase was higher in Peganum harmala (555.0{+/-}5.0 and 2597.8{+/-}0.4 units/g respectively). Maximum esterase and alpha amylase activity was found in Zygophyllum fabago (14.3{+/-}0.44 and 140{+/-}18.8 mg/g respectively). Flavonoid content was high in T. longipetalus subsp. longipetalus (666.1{+/-}49 g/ml). The highest total phenolic content and tannin was revealed in F. olivieri (72125{+/-}425 and 37050{+/-}1900 M/g. respectively). Highest value of ascorbic acid was depicted in F. bruguieri var. rechingeri (448{+/-}1.5 g/g). Total soluble Proteins and reducing sugars were detected higher in P. harmala (372.3{+/-}54 and 5.9{+/-}0.1 mg/g respectively). Maximum total antioxidant capacity (TAC) was depicted in Z. simplex (16.9{+/-}0.01 M/g). Pigment analysis exhibited the high value of lycopene and total carotenoids in T. terrestris (7.44{+/-}0.2 and 35.5{+/-}0.0 mg/g respectively). Chlorophyll a, b and total chlorophyll content was found maximum in T. longipetalus subsp. pterophorus (549.1{+/-}9.9, 154.3{+/-}10 and 703.4{+/-}20.2 ug/g respectively). All taxa exhibited anti-inflammatory activity as well as anti-diabetic inhibitory potential. Seed extracts of Zygophyllum eurypterum (96%) exhibited highest inhibitory potential, along with twelve other taxa of Zygophyllaceae indicated (96-76%) activity when compared with the standard drug diclofenac sodium (79%). Seeds of T. longipetalus subsp. longipetalus (85%) exhibited the highest anti-diabetic activity; other eleven taxa also exhibited inhibitory activity of -amylase ranging from (85-69%) compared with Metformin (67%) standard drug. Phytochemical screening revealed that selected taxa proved to be the potential source of natural antioxidants and could further be explored for in-vivo studies and utilized in pharmaceutical industries as potent therapeutic agents validating their ethno-pharmacological uses.

plant biology↗

bioRxiv2017

Comparative analysis of neutrophil and monocyte epigenomes

Neutrophils and monocytes provide a first line of defense against infections as part of the innate immune system. Here we report the integrated analysis of transcriptomic and epigenetic landscapes for circulating monocytes and neutrophils with the aim to enable downstream interpretation and functional validation of key regulatory elements in health and disease. We collected RNA-seq data, ChIP-seq of six histone modifications and of DNA methylation by bisulfite sequencing at base pair resolution from up to 6 individuals per cell type. Chromatin segmentation analyses suggested that monocytes have a higher number of cell-specific enhancer regions (4-fold) compared to neutrophils. This highly plastic epigenome is likely indicative of the greater differentiation potential of monocytes into macrophages, dendritic cells and osteoclasts. In contrast, most of the neutrophil-specific features tend to be characterized by repressed chromatin, reflective of their status as terminally differentiated cells. Enhancers were the regions where most of differences in DNA methylation between cells were observed, with monocyte-specific enhancers being generally hypomethylated. Monocytes show a substantially higher gene expression levels than neutrophils, in line with epigenomic analysis revealing that gene more active elements in monocytes. Our analyses suggest that the overexpression of c-Myc in monocytes and its binding to monocyte-specific enhancers could be an important contributor to these differences. Altogether, our study provides a comprehensive epigenetic chart of chromatin states in primary human neutrophils and monocytes, thus providing a valuable resource for studying the regulation of the human innate immune system.

genomics↗